Chapter 2 - Flying Free
Chapter 2 – Flying Free
Falkner, leader of the Violet City gym and possibly the most proficient Flying-type user in all of Johto, was not having a good day.
To begin with it had thrown a fistful of angry sages from the Sprout Tower at him as soon as he woke up, demanding an explanation for the disturbance in the weather that these past few days had the Tower sway like mad most of the time, forcing them and their apprentices to stay on the bottom floors and greatly restrain themselves in their training. “A day or two of your Flying-types playing around with the heavens is bad enough, but this has to stop,” Elder Li had huffed impatiently at him as Falkner, still in his pajamas, was rubbing sleep out of his face best he could.
He had patiently tried to explain to the normally wise and understanding elders that he had nothing whatsoever to do with it, and that aberrations of this level wasn't within his power to create anyway. Yes, his pokémon were well-trained and could probably bring about a decently sized whirlwind if they tried, and his Natu would be able to do even more once he had managed to train its psychic powers to their full potential. Covering all of Violet City in a ravaging storm for days without end was well beyond his capacity, and he would be surprised if any other trainer could, for that matter. Possibly Lance, but the prospect of the Champion of the Indigo League taking time off his duties to randomly screw up the weather of a small town in the backwater of Johto for no apparent reason was, frankly, quite absurd.
He had barely managed to get himself dressed before being ambushed by his twin gym trainers Abe and Rod, who basically wanted to ask him about the exact same thing. While his own Pidgeot and Noctowl were strong enough to maneuver the fiercest winds the skies could throw at him, his trainers' pokémon were in the same boat as his own Natu and Murkrow. For an entire week their training had been confined to the gym, and as spacious as it was it simply wasn't enough. Flying-type pokémon needed to be able to spread their wings in the open – it was how they lived, and the only way their trainers could learn to live with them.
With considerably less patience than he'd shown the Elder, he'd repeated his message to his subordinates – he didn't have any such power over the weather, he had no idea why it was happening, and he certainly wouldn't open the gym's wind shutters until the weather actually calmed down. They really should know better – they oversaw all of his battles against the trainers challenging the gym, so they were well aware of the limits of his abilities – and with all the time he spent with them, the bird keeper twins were probably closer to him than anyone except his own pokémon.
Not that there was a lot of competition, seeing as he was an only child with parents as distant as they came, but that was a different matter.
In sheer frustration at learning from his Pidgeot that the city's mayor was lying in wait right beside the pokémon center – to inconspicuously walk up on him with the exact same question as the others in mind, without a doubt – that usually was the first stop on his usual morning routine, Falkner stormed off east toward route 31 to vent some steam.
His Pidgeot came down to perch on his shoulder as he walked through the gate, and he patted its beak absentmindedly. The gate guard had a look of open disbelief on his face, but at least kept composure enough to keep the doors from malfunctioning on him. “Look at them, heckling you just because you've gotten bigger,” he said with a shake of his head to Pidgeot, who gave him an understanding coo in return. It was the first pokémon he'd received from his father, and the first one he'd trained on his own; he was hardly going to stop it from perching on his shoulder just because it had evolved once or twice. “They ought to wear a backpack once in a while. Most of them could sure use the training.”
Pidgeot cawed once in reply as they exited the gate, before taking wing to resume its usual scouting. The bird was restless by nature, but Falkner had taught him early on to use that gift for something worthwhile; nowadays, nothing ever managed to surprise Falkner.
“Pjyoo!”
Well, almost nothing.
The wind wasn't quite as fierce today as it had been before, but it still battered him with a good amount of force as he came out into the open. It was a refreshing feeling, if anything – Falkner had always enjoyed feeling the wind in his face, and since he'd taught Pidgeot how to Fly with him on his back, it had only gotten better. Today, however, it worried him. The sky was deceptively clear of clouds, but he knew well the feeling of low air pressure that heralded and followed any storm. And this storm had stayed for far too long to be natural.
“I need some time to think,” Falkner said to himself as he started to make his way toward the small lake that held his designated thinking rock.
The only problem was, he discovered when he entered the small glade at the north end of the lake, that for the first time ever since he'd discovered it, someone else was already using it.
Or rather, something else.
A strange, blue pokémon like he'd never seen before was curled up on the pointed slab of granite, gazing off into the forest with large, violet eyes. All the colors of the rainbow covered its mane and tail, and it bore a mark that looked like a tri-colored lightning bolt on its side.
More importantly for Falkner, however, it had wings.
Barring some mad twist of fate like whatever curious circumstance created Sudowoodo, this meant that he was looking at a Flying-type pokémon. A flying-type, and one of a kind that never had been seen before. He was sure about that part, at least – while he had never been studious enough to learn the entire pokédex by heart, it was his duty to know every pokémon of his own type, and he did not shirk his duties.
His careful approach did little to hide him from the typical sharp senses most Flying-types possessed, however – the strange pokémon swung its head around only a second after he'd spotted it, and immediately gained a wary expression on its face. It stood up, and to his surprise Falkner realized it hadn't been lying on the rock itself; rather, it was somehow standing on a cloud.
Its shape and size were rather similar to a Ponyta's, in some ways, but that was as far as his reasoning went in that direction. He had other things on his mind now – namely, to make sure his newest discovery didn't simply up and fly away on him. Drawing a circle in the sand under his feet as he assumed his battle stance, he whistled for his Pidgeot's attention and fixated the pokémon with a pointed finger and his best stare.
“You there! Pokémon! I, Falkner, challenge you to a battle!”
-/-/-/
Rainbow's frown deepened as the strange, blue creature raised its stubby claw at her and let out a gibberish of barks and howls. She hadn't gotten anywhere with her thinking yet, and before she knew it this weird thing had come up and disturbed her.
I haven't even had a chance to nap on this cloud yet! I mean, what gives?
She'd never been good at understanding random animals the way Fluttershy could, but when an enormous bird – larger than herself! – crashed down beside the weird creature, her confusion quickly disappeared. After all, there was no mistaking that wing posture – this bird was looking for a fight.
“Ohoho, aw, man. You sure you wanna take on the one, the only, the Rainbow Dash?”
A wide grin split her face as she started warming up her wings. She hopped off the tiny cloud she'd pulled together and made it disappear with a snap of her tail, and landed on the sandy beach with a dull sound. Smirking, she tapped her hoof against the big rock behind her, and made a low, taunting gesture with her wings at the bird.
“'Cuz, honestly, if you don't, you really chose the wrong time to stumble up on the world's fastest pegasus. I haven't even had my nap yet, and this has been a real crappy morning. I don't really think you've got what it takes to even come close to beat me, so unless you're really in the mood for taking the biggest defeat in history and rubbing your face in it, I suggest you take your pretty little tail feathers and run...”
With the single most offensive wing-gesture known to any avian, she tapped her hoof against the rock one last time.
“Chicken.”
The bird shrieked in fury as it charged at her with its wings flared, but she just took off and let it fly straight into the granite. It was a lot more agile than she'd expected, though, and banked up before it did more than clip its claws against the stony surface.
Well, this would've been real boring otherwise.
“What's wrong, ya dodo? Why're you so slow?”
She slowed her ascent just a bit to let her opponent have a chance at catching up. The bird wasn't sloppy, however. The moment she did it sped up tremendously, and she had to make a sharp bank to the right to avoid being rammed by one of its enormous wings.
“Alright, birdy! You wanna rumble? Let's rumble!”
With lightning speed she set off in an upward spiral around the bird's trajectory, trapping it in a fierce whirlwind. It only took several seconds before the thing managed to bank out, and it looked visibly exhausted. Its wings told a clear message, though – it wasn't done yet – and today, Rainbow Dash was not going to refuse that offer.
“Man squirt, you're looking awful tired over there! But don't worry, I've got just the thing to spark you right back up!”
Building up enough vapor to make a decent thundercloud on a day like this took a few seconds even for Rainbow, but with her opponent slowed down she had all the time she needed for that. Before long she was speeding along right above the surprised bird, who obviously had no idea where she'd just come from.
“Much – better – than – stupid – coffee!”
She slammed her hoof down on the cloud, and a jagged bolt of lightning struck her opponent right between the wings. The bird let out a cry of pain, and dropped several meters before making a sharp turn. First Rainbow thought it was going to run away and she simply banked upward in response, but realizing it was following her ascent in a spiral of its own she quickly recognized its pattern as a tornado spin.
“Using my own tricks against me, huh? You're one damn – cheeky – little – chicken!”
Breaking out of her ascent in an instant, she dashed downward. She found her target with ease, and her hooves connected with the bird's chest with a satisfying thump. Pumping her wings she kept speeding up, carrying them down together until she was only a few meters above the lake's surface, where she gave a final push with her hooves and thrusted the great bird into the water with an enormous splash.
Satisfied with the result and fairly sure her opponent was all finished, she gave her wings a few steady beats and looped around, landing on the large rock she'd started on with a loud noise.
“You had enough yet, you stupid overgrown chicken?”
She wasn't really angry at it – she was actually rather thankful for having someone to vent her frustration at – but as far as frustration went, there was plenty more of that emotion buzzing around in her head thanks to this stupid morning. She was hardly going to run out any time soon.
In all the ruckus of her duel, however, she'd forgotten all about the strange blue creature, however. She heard it bark, and before she knew it a bright beam of translucent red swished past her. It shot into the roiling waters of the lake with an eerie sound, and suddenly she could make out the form of the big bird, shining with the same color for a few seconds before disappearing entirely.
She swung her head around and stared at the blue creature, who was holding some sort of ball in its hand. “Hey! What sort of creepy magic was that supposed to be? And what the hay did you do to that bird anyway? I mean, sure, it lost the fight, but come on!”
Conversation was fairly useless at this point, and she knew it, but if some weird magic creature was going to start flinging spells around she needed to distract it before she could escape. As fast as she was, she knew well how easy Twilight could catch her if she wanted to, and she wasn't going to take any risks with this thing either.
The creature grunted something in response, and fastened the ball at its side in some sort of belt-like device. Now that she could get a closer look, it was probably just wearing blue clothes – it was obviously fabric, not fur or skin covering its midsection. She'd been a bit confused by its pale blue mane at first, but it was clear enough now that she thought about it that its skin was actually of the same pink color that covered its face. It looked like a strange, skinnier version of Harry the bear, without all of his fur.
Rainbow didn't have much time to think about this, however. The creature retrieved a second, identical ball from its belt and threw it into the air. There was an explosion of the same red light as from before, and suddenly there was a massive owl standing before her, even larger than the bird she'd just fought.
Once the initial surprise of having yet another enormous avian appear in front of her subsided, however, irritation took its place with gusto.
“Oh come on! Why didn't you just bring this guy out to help in the first place? You might've actually gotten a few hits in on me if you teamed up, you dorks!”
The owl didn't respond to her taunts, however – it simply stared at her with the same, unreadable eyes that had always made Owliwiscious seem rather creepy to her.
“Oh, noooo, you're staring at me, I'm so afraaaid. Whaddya expect me to do, fall down from...boredom or something...?”
For some reason she couldn't even begin to comprehend, Rainbow Dash felt very compelled to do just that. Just lie down and snooze for a bit. Take a nap. Yeah, that felt like a really good idea. A really, really, really good idea.
“Wha... don't think this means...you won...'r n'ythn...”
Just take a little nap. I haven't had mine yet. I need to sleep. Sleep right now. Sleep. Right. Now.
An enormous yawn cracked her jaws, and in the corner of her fluttering eyes she could barely spot the bear-creature holding yet another of those ball-things.
A vague movement of one of its paws was the last thing she saw, before the world disappeared in a flash of red light and she fell asleep.
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Nice, can't wait for more.
So your telling me she got captured.
Hmm. Taunt, either Gust or Hurricane, Thunderbolt, and Stomp, if I'm reading this correctly. Interesting. I'd be surprised the Pokéball worked on Dash had you not indicated that the ponies (and dragon) had types, and were thus subject to the same game mechanics as Pokémon. Now I'm more interested as to why it worked. And how Rainbow's going to react once she wakes up. Bearer of Loyalty, faced with a new master. What now, Dash?
Soo apparently the total word count is fucked up...obviously more than 4.4k words
2234585
Yeah, I kinda wrote that A/N in the middle of the night after a bad case of food poisoning, so I wasn't really in the most stable of moods. I'll see if I change it at some time. anyone who likes Arceus is still a faggot though
Granted that we won't have any of the Pokémon Deities appear in this fic, though (this I can bloody well promise), we won't have to worry about that particular power level issue. I'm well aware that in terms of sheer power, there's not much of a contest. However, in-game Mewtwo is still a far better special sweeper than any of them, and all things accounted for it's just a Lot more awesome.
The Thaumatron was never really meant to be much of a thing, really. It's a bunch of spinning metal rings with one of Twilight's big computery thingies attached to them, and a big runic circle on the floor. That's pretty much it.
Reg. typings: you're actually pretty spot-on with most of these, good lad. Well done! Besides, I did say I was going to reveal the typings of our dear cast members in this chapter, so...yeah. Here you go:
Twilight - Psychic
Applejack - Grass/Fighting
Rainbow Dash - Flying/Electric and all the Zapdos fanboys in the world squealed in joy.
Fluttershy - Flying/Psychic
Rarity - Rock/Psychic
Pinkie Pie - Ground/Dark
Spike - Dragon
Twilight, Spike AJ and RD were pretty easy choices to me. Besides RD being able to manipulate lightning with her clouds, there's also the fact that light itself is also ultimately electromagnetic radiation. Even if it doesn't make the Sonic Rainboom an Electric-type attack, it's a lot more logical than any of the other choices I had. Besides, who the hell wants to be a Flying/Water type anyway? x4 weakness to Electric sounds pretty illogical for someone who's responsible for managing the weather to me.
Fluttershy was a fairly easy choice as well - Flying type is obvious, and while I first thought of making her a Normal-type it just didn't seem fair to her. Reflecting on her Stare, her empathic abilities and other things (weakness to "bad things" meaning Dark-types for one), the Psychic-type just seemed the right choice for her.
Rarity was a bit of a tossup between Steel and Rock, but it didn't feel logical to take away the obvious Tom reference from her - besides, what sort of gemstones do you find in solid metal chunks anyway? We're getting a bit filled up on Psychic-types, but honestly, I don't really give a damn at this point ^^
Finally, Pinkie Pie. No, I'm not going to pull a Full Insanity Mode With No Limits on her and give her some invulnerable crazyass typing combo, nor am I going to invent a new one for her. Ground, because she's an Earth pony, who is not very good at handling plants but quite capable of farming rocks (Ground > Rock). Dark, because Pinkamena. You don't need more explanation than that.
Hope you all enjoy the chapter, people!
Eh, something about the mane 6 able to get captured makes me feel uneasy and wrongish. Good story regardless, just not my type it seems.
2234628
More like Aerial Ace or Extremespeed or something over Stomp actually, and the use of an actual thundercloud is more towards Thunder, but yeah, that's the idea of things.
Like other obviously sentient/"intelligent" pokemon however, she's blessed with a lot bigger movepool than just 4 at once, and I don't think you need to guess twice for what her signature move is. :)
2234629
Probably derped since I just posted the new chapter or something? W/E.
uh i hate to point this out but there not pokemon and pokeball technology well brake in an attempt to contain something other then pokemon. i qoute the show where ash caught a donut and then the pokeball popped open in a busted fashion.
The mane 6 being captured is fresh and original! good job!
2234669
In case you managed to miss the fifty times I wrote it already, This Is Not The Anime.
Besides, what's to say what exactly classifies as a pokémon anyway? It might as well be "any form of biological or artificial life that's not human" for all we know. Ponies surely fit into that category.
2234669
I'm not too sure on this, but I think he said he isn't following the anime canon.
2234678
Perception is a virtue. :)
TL;DR this follows game canon, with very small modifications to allow for the story to progress properly. Power level references can be made to the anime, but that's simply because we have very little else to go on.
A Mewtwo story? Schweet. I think I'll still am going to be the only dude that's gonna make a Pokemon Xover without Pokemon.
2234705
OH HORRIBLEST OF POKEMON, WHY DO YOU EVEN EXIST
Magikarp at least has an evolution. Mawile at least has one of the coolest designs in pokémon history. Sableye at least has the best typing possible.
DUNSPARCE, OH DUNSPARCE. I remember catching you back on my first Sapphire run and starting to train you, hoping that you'd evolve into something awesome. BUT YOU DIDN'T, AND YOU WERE TOTALLY USELESS.
Excuse me, I'm going to go cry in a corner now. ;_;
2234725 Sorry pall, but I'm useful. Here's a quote from Smogon university, the main base of Pokemon and Pokemon Competitive Battling.
EDIT: and IDK what your saying, man. I relied on Dunsparce to take down Ghetsis's Hydreigon and it worked perfectly.
2234734
NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
EDIT: J/K, paraflinching is lame and NU is kind of hipster tier, but I know what you mean. I used Froslass myself, much to the same effect, and she's somewhere around the same area in terms of competitive usability...
her design is galaxies better though
2234751 Here's a quote from Serebii, the OTHER main Pokemon database:
Your Dunsparce just sucked is why you hate it.
2234751 As long as you admit Dunsparce is at LEAST mediocre and usable, I'm fine with it. You say Charizard is amazing then we need a little chat. I've OHKO'd a Charizard with Dunsparce.
EDIT: NU isn't a hipster tier, really. It's just the tier for lower Pokemon. In my opinion, overused is lame and boring and paraflinching is incredibly fun.
2234669 I'm pretty sure pokeballs *can* catch anything, they're just programmed not to capture inanimate objects and people. In Pokemon XD you hacked them to let you capture pokemon already captured by other trainers, for example. And anything can be put in the item storage system which seems like the same technology.
Aliens are definately pokemon by default anyway -- look at Clefairy.
2234761
I have a shiny dunsparce.
2234643 Maybe Flying/Ghost for Fluttershy? Ghosts get a lot of fear-based moves and it means most animals (normal type) wouldn't be able to hurt her.
Of course she's not dead.
I read somewhere that pokeballs were designed to catch pokemon, but actually that they can catch pretty much any sapient non-human lifeform, and that last restriction is programing based.
So in essence, humanity developed the ultimate trapping, sample-taking, and etc. device, and use it to play a freaking game. In their defense though, better that then use as a torture device.
I don't know why, but the ponies being able to be caught irks me a bit. That just seems to create an unnecessarily large issue, what with them not even being able to communicate with the people that are trying to get them to suffocate in those damned pokeballs! I'm just wondering on how the Johto protagonist is going to come into play, and Gary(or Blue, whatever you wanna call him) of course, since he's mentioned in the description.
If there is one thing I can say about them being able to be captured, it does make things incredibly interesting. I'm sure despite the fact that they can't communicate that Twilight will obviously figure something out eventually to get her friends away from their Jailers. The question is: What will the something be? Only one way I'll find out of course.
But yea, despite the -only very slight- problem I have with the Mane 6 being able to be caught, I'm really liking this so far and will be reading it all the way through. But please don't tell me that all the next few chapters are going to be about various of the Mane 6 getting caught.
That would be pretty repetitive.
head canon excepted. I now view the mane 6 as legendary pokemon.
2234880 Mother hugger I'm jealous.
I want morrreee but i can be patient yes of course..
but really amazing work so far. Cant wait for the next chapter!
hmm im listening i wonder what she will do probably fly away first chance she gets and PLEASE give her a silly nickname FOR THE LOLS
I want this to update quickly so I can see how Rainbow Dash reacts. More than likely, she'll try to beat him up for capturing her. And PLEASE don't make her friendlier to him because of how pokeballs make pokemon automatically follow the trainer's every command.
2233746
Can't find the 9th, 13th, 14th or the 15th movies anywhere.
Hmmm... not sure I like that ending too much. Then again, such is the nature of a cliffhanger.
Poke and Ponies. My to favorite things.
AUTOMATIC FAVORITE!
(plus I like to see where this leads)
2234941
This is kinda of bothering me as well. The idea of the Mane 6 in pokeballs does not sit well with me. Hopefully you can do something to assuage my concerns, as this does appear to have some potential.`
2234643
Everything is correct about the pony types except Twilight! She should be Psychic/Fire for obvious reasons!
I'm definitely tracking this story. I can't wait to see what happens next. The 6 ponies being taken in pokeballs was unexpected, though I don't think it will change their minds and bind them to trainers like pokemons are, right?
Id like to second the twilight being psychic/fire idea. If only because she does that flaming rageshift thing in the pinkie sense episode.
2235144
That would make an interesting issue. Since he is Loyalty, the pokeball will have an effect on her, making her loyal towards Fawker? Or being an Element will prevent her to be subdued to the pokeball nature?
Thumb up, fav and moustache
I'm calling it now; if at least one of the others gets caught, then I bet that Rainbow ends up having to battle them at some point. Question is, what happens then?
I know many of the readers here will automatically disagree with me on the grounds of Pokemon + Ponies, but I dislike this story.
For one thing it is written with a very brash and simple style. This is not always a bad thing, but when there is no subtlety I find it hard to keep interest in a story.
Another thing is the character personalities. So far there seem to be only two. Twilight, Rainbow, and Falkner seem to share the same exact personality traits. Interestingly enough, they sound just like the author notes. And while we have not seen enough of the other characters yet, the descriptions so far fit into one of two types: a copy of the author or a fool. Hopefully the other characters will have their own personality rather than being copies of the author.
I don't think it's a very good idea to split the story into six directions right off the bat. This will make you divert the reader into six separate stories until they re-converge into the main storyline. Of course I could be mistaken and one pony will take all the attention...
And on a more personal note, I really dislike the concept of poke-balls. It's simple slavery. Hit a sentient creature with one of these and they will be forced to obey you for until you release them.
The others will be caught, and they'll have to fight each other. Of course, there's no way they'd actually go along with it unless pokeballs brainwash pokemon as well.
2229316 It's okay, no-one really cares about spike
WHAT DID YOU CRAZY PEOPLE DO TO MY STORY WHILE I WAS OFF FOR 5 HOURS LISTENING TO RANDOM MUSIC AND DRINKING CIDER? >_>
So let's see here. Comment corner in the middle of the night, because I'm like that. Here we go...
2235437
Mewtwo learns Aura Sphere by level up if I'm not wrong, so while Genesect can probably hit it pretty hard, that's - actually all three of the ones you mentioned are - event-only pokémon versus a pokémon that has been in the game since Gen1 and is capturable in 10 games in his original cave, and has ordinary level-up moves that can counter most of their shit.
Again, though, this is just metagame abstraction shit, and you can be sure as hell no trainer in this fic is going to randomly catch himself a Genesect/Arceus/Darkrai out of nowhere.
2235633
But that would reveal her secret identity as a mutated Ponyta to everyone! Nobody must know the truth! NOBODY.
2235236
TokyoToshokan is your friend, as it is mine.
2235929 On your pokeball statement, pokemon don't always listen to their trainers when caught, Ash's Charizard never listen to him and in fact burnt him to a crisp a couple of times. There's also Iris's Excadrill and Dragonite, one who will always sleep in battle and the other that acted on it's own. It took a while before these pokemon started to work with them. If you want a video game example, unless you have the proper badge, your pokemon wont do the attacks you want and might do 3 other things 1. Not listen thus wasting a turn 2. Do random attack (they might do the attack you choose, but I nerve seen that happen) and 3. Go to sleep. If you have anymore questions please ask
So will the ponies be able to decide "fuck that" to being in pokeballs like what Psyduck and ect could, or will this story take on an unexpectedly dark turn? To find out tune in next time, same bat-time, same bat-channel!
I also wonder just how many badges a trainer is going to need to be able to control the likes of Pinkie Pie.
2236355
The game example actually only ever occurs with traded pokémon, since it assumes that those are the only ones you'll have problems with conflicting loyalties with. It'd be awesome if it didn't treat that lv56 Steelix you just caught the same way as it does the lv49 Venusaur you raised from the game's start...
Welp.
I guess I can spoil that much for you, however - no, this is not a story about how Rainbow Dash gets mindraped by a Noctowl (you can hear yourself how stupid that sounds) and turned into Falkner's newest uber. That would be incredibly tacky (and stupid). She will remain herself regardless of whether she's been caught by some strange magical device by some weird alien with a bunch of freaky birds or not.
As for the format of these, I'm going to go through each of the Mane 6 in a separate chapter to start with, and then we'll start moving out from there. Hopefully that won't take too much time, however.
Rainbow Dash Possibly Getting Caught!
Why do you let these things happen, Why!!!
hopefully she doesn't get caught and then she wouldn't won't have to get tested and stuff like that
dammit noctowl why!!!
2236367
What's that? You mentioned "control" in the same sentence as Pinkie Pie, and it wasn't anything in the direction of "Pinkie Pie has no self-control" or "Controlling Pinkie Pie or her abilities is scientifically impossible"?
My word, I think we must refer you to CAVED
2235144 if you do that we will kill you
Well, this story is at a crossroads. I get that you say this isn't the anime, but still, that's hella sketchy, the ability to capture the ponies in Pokeballs like that, especially since they don't work a thing like Pokemon in their own universe.
Given what you've said about how the ponies' "typing" is going to work, that suggests something to me: that they're all different species. See, in canon, since Unicorns, Earth Ponies, and Pegasi can all interbreed, they are different subspecies, but otherwise are all the same species. And you don't see different, say, Caterpies, exhibiting different types the way that the Mane 6 currently are. And even if you were to say that they were all different subspecies and that this corresponded to how you can breed different Pokemon, such as, say F!Machoke with a Hitmonchan, or other such pairings, that still suggests weird things about the pony world. Does that mean that all ponies, were they to cross over to this world would be different (sub)species? Is Thunderlane a different species from Spitfire? Are any of the ponies then incompatible to breed the same way some Pokemon are? Does that mean that if two ponies happen to land on the same type that they are identical or just different (sub)species of Pokemon who look incredibly similar like Feebas and Magikarp? And if Zecora were to cross over then what would that entail? IRL, Zebras and horses cannot produce fertile offspring. Would that make them incompatible breeders or would the offspring suddenly become compatible or what? And speaking of offspring, How does one justify Pinkie Pie, whose parents are probably rock types in this universe, being ground and dark? Do two different (sub)species of pony give birth to an entirely different (sub) species of pony? And after you've considered all that, then what does this suggest about the nature of regular Pokemon? Why do they all seemingly look exactly the same save for a few discrepancies between male and female? Are they all clones or something? Why are certain Pokemon only compatable with others then?
I'm sorry, but this just raises a ton of questions. I get that none of this will probably become relevant in the course of the story, but honestly, before you go making the claim that the ponies can be caught by Pokeballs, and therefore basically are Pokemon, then you have to consider every angle. To quote Bruce Wayne, "It just raises too many questions."
And after all of that, there's still the undertones of slavery and mind control that permeate the very concept of Pokemon. This sort of thing can generally be disregarded, at least in the games, since it's never really made clear in-game the levels on which Pokemon think (in fact, it's suggested that at least most are basically animals in-game as opposed to the anime). While there are some Pokemon, like Mewtwo or Alakazam and maybe a few others that are suggested to be sapient, most aren't suggested to be such. Now you've got a lot of work ahead of you, trying to justify this now that you're applying it to ponies.
I guess ultimately the point is that you got some 'splainin to do, Lucy. A lot of this COULD be explained. For example, if you take the idea that all Pokemon are aliens (a theory posed in the anime, though I'm not sure about the game) and say that they were wrong about them being from the moon or something, and instead all Pokemon are interdimensional aliens, that might work. If you suggest that the Pokeballs are designed to catch beings that, say, vibrate on a different dimensional frequency than humans. That would suggest that any interdimensional alien could be caught with a Pokeball. It would also clear up the typing/breeding issue, since who knows how aliens work in other dimensions. "Pokemon" or rather Ponies just work differently in the Equestria dimension to how they work in the dimensions the Pokemon are originally from.
And the mind control thing could be explained away by suggesting that there is no mind control. That the only reason that Pokemon(assuming they are sapient) tend to obey their 'masters' is because of a sense of honor. Like 'you bested me, now I am your servant' or some mindset like that. And that's the reason why Pokemon sometimes disobey orders if they are too high a level, because they feel their 'masters' are "no longer worthy" or something. Such a mindset would be alien to Rainbow Dash, and she'd probably be permanently disobedient. It could also be explained that they only thing a Pokeball does is put a sort of 'leash' on the Pokemon. Still creepy and morally objectionable in some ways, (especially when trading is brought into account) but it would otherwise work.
I also have to wonder why, if they are both Pokemon, Rainbow Dash and Pidgeot seemingly couldn't communicate. Again, could be explained away by the whole "alien" thing, but still... it would make things a lot easier from a narrative standpoint if the ponies could either talk to the humans or to the Pokemon.
Lastly... there is no way that a Pidgeot could sit on a shoulder. Not unless you were, like, the Hulk or something. Those birds are freaking BIG. As in, 'bigger than people' big. How is that supposed to fit on a shoulder?
Anyway... I'm skeptical of where this story is going to go. This is something that could make for an excellent twist and add a lot to the story, but it has to be tread carefully from this point on. Because the undertones of Pokemon are very much NOT friendship or magic and one wrong move could make you lose, like, ALL of your readership. I can already see that the dislike bar has doubled since yesterday (though admittedly, the like bar is much bigger), and a lack of explaining things, or explaining things in the wrong way, could lead to huge problems with the overall tone and evolution of the story.
UPDATE!!!!!!!!!!!!
MOAR!!!!!!!!