You know, a good chunk of the discussion with VAmpDash over Magicae ex Machina has been around what mecha goes with what character. And although there's a short of official list in the Source Book, I think it would be nice for the group if we all get a said on this. Since only the Main Cast (that's the Mane Six plus sidekick) I'll post here the reasoning behind it.

Twilight and Trixie / Gundams Wing and Deathscythe
For Twilight, I had a ver specific image in mind: The Wing Zero from Endless Waltz extending it's wings in space. Then, I realized both, Twy and Wing share a lot of common traits as the titular pony/mecha of their respective series. The hero, extremely powerful, strong and skilled, and so on, to the point that both get a radical upgrade (Alicorn and Z.E.R.O. System) that puts them above their companions in power levels, without leaving their side.
Then, comes Trixie, Twilight's kinda sorta oposite, which is the same relationship Deathscythe shares with Wing (and Duo with Hero for what it matters). When reading one of the Gundam Wikis, I came into a part where it explained that the Deathscythe's basis was psychological warfare, hence why it looks like the Grim Reape, to strike fear into it's opponents' hearts. That, combined with the Hyper Jam system and the fact it was built as an stealth model, gave me the impression that this Gumdam basically uses weaponized illusions. That was just it and I put Trixie inside the Deathscythe.

Applejack / Red Baron
It must be hard being Applejack. In a group where other fly, have magic and break physics, she's the one with no powers... and she still kicks ass when the occasion calls for it!
From there, I got hellbent on giving her a robot with no weapons whatsoever, and that's when I remembered the Red Baron. A fighting mecha with no weapons beyond a super heated punch and its skills. Sure, some may point out that most of Real Robots would have worked as well, but that's the beautiful part. Red Baron is in a half-real, half-super setting, and it mostly has to go against super robots, various orders of magnitude over it. Granted, the Sleipnirs from Aldnoah.Zero work on a similar concept, but the Red Baron has even less weapons.

Rainbow Dash+Lightning Dust+Gilda / Getter Robo
Okay, if you guys had to describe RD in one word, what it would be? The top three across the fandom and canon seems to be "hotblooded", "stubborn" and "fast".
At first we were going for a Valkyrie, as those are practically some of the fastest mechas in fiction. But then, VampDash pointed out that as hotblooded as RD was, there was really only one mecha fitting for her; The Getter Robo, which actually runs on that thing (and let's be honest, no one would be surprised if Rainbow starts acting like Ryoma).
Of course, that lead to the obvious question "who goes with her?". The original idea was Rarity and Applejack, but that would have limited their own characters as just sidekicks of Rainbow, so we moved on to other Rainbow related characters, which are Lighting Dust and Gilda. Lightning, as the one physically similar to Dash, got the Getter 2 and Gilda, who looks bigger in comparison, got the Getter 3.

Rarity / Big O
This one came to mind immediately. So far, I've had to give very little explanation on this one because everyone seems to agree that Rarity would make a great pilot for Big O.
Big O is one of those mecha series that got stuck between super and real robot, but not only that, as the series itself is hard to categorize. Dieselpunk, Noir, Mystery, Post-Apocaliptic. However, there's one thing we can say without questions; Roger Smith is the bastard child of James Bond and Bruce Wayne. This got us a working ground of the Big O's pilot being someone of wealth and taste, and that pointed straight at Rarity.
It also works in reverse. When you see Rarity, is hard to think of her inside a giant robot fighting other equally big threats, so her mecha has to be something out of the box for her. And as stated before, Big O is so out of the box, that it came back and smashed said box till the metaphor lost any sense.

Fluttershy / Dragonzord
The idea spammed around Dragonshy, and around Fluttershy being a beastmaster herself. The initia thought was that Flutters needed a mecha that wasn't ambiguously sentient, but 100% confirmed to be alive. That reduced the area of work to two quite specific areas; Zoids and Zords.
Then came another concept, the "beware the quiet ones" trope that Fluttershy embodies, so we rolled with the idea of giving Fluttershy the most dangerous mech possible without being a game breaker. That's ende up being the Dragonzord.

So, with those criteria as a base, what mecha would you give to what pony?

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I'll try my best to be up to standard, but let me start with what I distinctly see is lacking here so far:

Pinkie Pie / Boss Borot: Boss Borot sample
Actual show Boss Borot sample
Is it an obvious choice? Is it too unusual? What IS Boss Borot? Well, I'd like to think I'm familiar enough with it to know that in the original shows itself it's an awkwardly functioning mecha that's technically a Super. At times, it tries to fight straightforward(and maybe not do too well), at other times it tries some really really out of the box ideas(that often fail). It could be the pilot's doing, but then there's the numerous game appearances; It's either really good, really bad, or just right in what one can get out of it. So... generally unpredictable in its potential output overall. That's why I think Pinkie might be a good fit for it; With her resourcefulness, she just might be able to tap into its full potential frequently and really make it shine with out-of-the-box maneuvers she can handle with ease and her own kind of unique grace, and probably get it customized for varying scenarios based on who else might be co-piloting with her(possibly her sisters).

Celestia / Angelg: Angelg sample
It's a Super, fairly agile, tough, and great in both short and long range offense on top of being elegantly designed; Surely a perfect fit for a Monarch/Diarch, no? Celestia might come off overall as one who would prefer peaceful solutions of course, but when the going gets tough, she's also one who would certainly take the fight to her foes personally, and the Angelg can certainly handle being in almost any situation in battle. Plus, its ultimate attack is a giant exploding flaming Phoenix shot; Could it be any more fitting?

Luna / Granzon: Granzon sample
More or less as effective in combat as the Angelg, with a darker regal-looking design. Luna I'm less certain of how she would act in battle compared to her alter ego Nightmare Moon, but I would assume she'd be just as aggressive if she were in combat without losing her mind(though more careful about collateral damage at least). The Granzon certainly has power in spades, and to compliment Luna's dreamwalking ability, can virtually move through dimensions to attack her foes with her own brand of nightmarish patterns if need be. Plus, its Ultimate move involves an all-consuming darkness either in a broad field or against a single target. Fitting counter-part to the glimmering Angelg, no?

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Sorry the late response, long, long couple of days.

I'm loving the Idea of Boss Borot sticking around, but I'm not so sure of giving it to Pinkie. The concept sounds funny, nad Pinkie could probably pilot the Borot in a way it could defeat Unicron. However (very sorry), I think Pinkie and the Borot contradict a little each other, as in both are joke characters, Pinkie is the trickster type while the Borot is usually the resident butt monkey. We will have to really think this one through.

I recommend you to see the plot-lines of Season One in the forum so you get familiar with the fic's tone.

Now, on Celestia and Luna, I'm all the way down with it, so if you have a good story (short or otherwise) feel free to do it and it will probably end in the official canon.

See ya.

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Alas, I currently lack the time to get familiar, much less get more involved in the setting, to offer much else. I suppose I could add another suggestion to Pinkie under that assessment however; I am glad you like my suggestions for the Royal Siblings at least.

Perhaps one of these mechs will suit her more?
Fairlion (Type S and G) She does like singing and dancing quite a lot after all, though I am unsure who would pilot the other twin mecha if you wanna use two.

Fei Yen (Alpha 3)
Fei Yen (UX) Yes, the UX version is exactly what it looks like.

Walker Galier (Z2) Oldschool hot-blood with a side-dish of silly.

By the by, Boss Borot could be piloted by the likes of Flim and Flam. Also, I thought of one more mecha pair with a possibly fitting pilot.
RX3 (Z2)
Victory Deluxe (Big O) Hey, if Rarity gets Roger's Big O, why not give Blueblood one of Beck's tacky/gaudy/cheesy big flops in contrast?