Let's make a game: Doing a list of all the plot-holes of the movie and also of how many convinient things happens, just to have an idea.

1. Why are they in the crystal empire? There is literally no reason to be in the crystal empire. At all. Wouldn't a royal inauguration for *hack* PRINCESS SPARKLE take place in... I don't know, EQUESTRIA, as in, CANTERLOT?! But nope, we made this crystal empire last season so we're going to abuse the fuck out of it until you're tired of it.
2. Celestia has a former student she's expecting back, so she doesn't' think to have anyone guard the only way too and from the mirror? Especially on this night?
2.a ... or for that matter, PRINCESS SPARKLE?
3. Why did she keep a potentially dangerous mirror to a potentially dangerous alternate dimension around anyway?
B (I don't want to renumber everything): How in the hell did sunset even know about the crown/twilight being a princess/that she'd be where she was/etc? She apparently left before the whole nightmare moon thing, and she's (assumably) been in high school land before then.
B.1: where did she stay that whole time? I mean, twilight had to sleep in the library, where did Sunset shimmer live?
4. None of the Main 6 use their abilities to catch Sunset. Rainbow dash can fly fast enough to cause sonic rainbooms, but not catch a unicorn?
5. They waited till morning to explain it. I can see the need for beauty sleep, but COME ON! You only have a limited amount of time.
6. Celestia's explanation as to why the main 6 cant go with her is BULLSHIT. I mean, the mirror takes you to an alternate dimension, not equestria several hundred years ago. Spike clearly proves it bullshit by diving in after twilight anyway.
7. Twilight just doesn't happen to know that the bully is Sunset Shitter. Despite anyone with working eyes being able to spot that ketchup-mustard colored hair a mile away.
8. Spike is a dog, Twilight is a human, yet all of fluttershy's animals are still animals.
9. The Cutie Mark Crusaders should not be attending high school.
10. Twilight never thinks to simply steal the crown back (It's not theft if it's yours to begin with) or reveal spike the talking dog to prove her point. Nope we gotta do things the cliched way because cliched high school plot demands we win the prom. (Fall Formal, but really who cares? Call it the Fart Fuck-all for all I care)
11. Flash Sentry. Okay, I'm just going to get this one out of the way sooner than later. He's useless. They never have any meaningful interaction, they never talk about anything, they never learn each others interests. He never plays any meaningful role (except for one scene which is itself a stupid plot-hole and convenience, which you could replace him with literally any character and it wouldn't be an worse. Actually it'd be better). They just bump into each other and blush. I've seen boxes of Cherrios that were less bland than this annoying twat. Yet hasbro keeps shoving it in our faces that this is the love interest, like "HAY GUIZE THEY'RE TOALLY CRUSHING ON EACH OTHER TROLOLOL SEE HOW SHE BLUSHES AND GOES GOOGLY EYED TROLOLOL SEE WE MADE HIM BY READING SELF INSERT FICS ON FIMFICTION.NET! THE ONE WE GOT THE IDEA FROM HAD A LARGE RED BAR AND LOTS OF THUMBS DOWN! THATS GOOD RIGHT? DUR HUR! SEE DAY IN LUV HUR HUR BUYOURSHIT"
Seriously, people on Derpiborru often make the joke "still a better love story than twilight". Well guess what? It's not. It's WORSE than Twilight. And when your love interest makes Edward Fucking Cullen look like James fucking Bond, you know you have problems.
12. Sunset shimmer explains what bringing the crown into this magic-less world does... without actually explaining anything.
13.Twilight sleeps in the Library. No one notices, no one cares. When in an even halfway realistic world this would get your arse in a jail cell faster than you can say "pony".
14. The whole "Sunset made a video of twilight being incompetent" comes and one scene later everyone promptly forgets about it. I know high schoolers have a short attention span but COME ON!!
15. The main 5 all broke up over the stupidest thing and not once thought to sort it out...
16. ... which they promptly do by themselves in front of OH SO WONDERFUL PRINCESS SPARKLE.
17. Flash's connection as Sunset's ex is brought up, and never comes into play ever again. (If it was Shining Armor's alt world counterpart like i'm pretty damn convinced that it was going to be, this would at least make sense as it would show what might have become of Shining had he never found or been seduced away from Cadence.)
18. Twilight suddenly becomes popular by doing a dance number. Which works because "DUR HUR HI SKOOLURS R DUM".
18.a . Which is all rarity's idea, not hers.
19. Sunset ruins the gym, then frames twilight for it. HOWEVER, it's revealed that she needs the fart fuckall to proceed as normal. So this plan makes absolutely no sense, other than to show "LAWL SUNSETS A GENERIC INCOMPETENT BITCH"
20. She fools Vice Luna with GLUED ON CUT OUT PICS. Between that and not questioning where Sunset and/or Twilight's lack of background, she is easily one of the most incompetent vice principals ever. Right up there with the ones that try to peddle creationism in schools.
20.a Which doesn't even make sense in of itself considering that one would have to fit perfectly behind "twilight" for it to work. Or have mad photoshop skills (which thanks to the cut outs we see is clearly not the case.)
20.b This issue comes and goes within half a minute and is yet another drive by problem.
21. The dance has to be moved to the following night as a result of the gym being wrecked. Which means twilight (or sunset) wouldn't get the crown back until the portal has closed. Which ruins sunset's plans. GOOD FUCKING JOB.
22. The problem of twilight telling the others the truth is resolved by OOC Pinkie Pie. Seriously, this is bullshit. There's leaning on the fourth wall, and then there's just pulling shit out of your ass. FFS, this "hunch" crap is worse than dimension-traveling super pinkie in Sonic Rainboom, which even Josh Scorcher who practically invented the term "It's pinkie pie don't question it" called bullshit on. Either way, it's just another drive-by problem.
23. Spike talks to rarity, showing just how twilight COULD have gotten the crown back from celestia (and still could) if she wasn't a goddamn moron.
24. Everyone just suddenly drops everything and pitches in to clean up. Nevermind classes or anything (oh wait, nobody is actually attending classes in this school. I forgot.)
25. Sunset lets spike go after kidnapping him. What the hell was that for?
26. Sunset then threatens to destroy the portal with a sledgehammer. Haven't we already established that objects would just go right through? I mean this might work if the portal was already deactivated but not while its still active.
26.a: And don't give me this "smash the frame" bullshit either. Have you ever attempted to hit solid concrete with a heavy sledge hammer? let alone a small one like that? not only is this hard to do, but odds are your not going to do any real damage in the first swing.
27. Twilight refuses... not by calling the bluff, but by saying that "Equestria will survive without my element of harmony" which has multiple times throughout the series (including at the very beginning of this movie) proven to be absolute bullshit.
28. Sunset gets the crown after twilight tries to play keepaway (rather than JUST TAKING THE THING AND MAKING A RUN FOR THE PORTAL, YOU TWAT).
29. ... Really sunset? You're going to take over equestria... with an army of <1000 strong zombified, untrained, uncombat worthy TEENAGERS?! My fucking god sunset.
30. The "elements that created it" asspull. Need I say more?
30.a: S4 Pilots proved this to be an even bigger asspull than people originally thought. It proved that YES the elements ARE the gems and not some "soul thing" or whatever, and YES without the gems the Main 6 can't use them, and that YES the stones that NMM destroyed in S1 EP2 WERE the elements of harmony and not just representations or whatever. And that YES the writers were pulling this shit out of their ass when they came up with this "elements that created it" crap and simply didn't give a damn anymore (if they ever did.)
31. Sunset does a heel-face turn (or was it face heel turn? I get that confused) right out of nowhere.
31. Yes, time is of the essence. so let's waste that time in a pointless dance sequence and get back at the very last second.
32. Fuck you Flash. Seriously, Fuck you.

There that's the ones I can think of. Not my best since i'm half asleep when writing this, but oh well. I tried.

2150692 my biggest issue: THEY HAVE GOD DMN MULTICOLORED SKIN! They are humans yet "oops I have purple skin" is okay.

Even with the weird skin, Luna doesn't look like Luna.

Why do they have so many horse headbands and tails?

If this is supposed to be a magicless world, I can understand the transformation of Sunsht Shimmer, but why do the mane six grow ears wings a tails?

If the mane 6 grow wings, where are the horns?

Twilight has pony ears, a tail, and wings, but people are paying attention to her dancing.

NO LYRA!!!

2158172 One thing that i've noticed.
When Twilight gets interrogated by Human Luna, accused to have wrecked the gym, where was the HuMane 5? Were they near to defend Twilight, just like real friends would do especially if you are witness of Twilight innocence? Nope. Once that Twilight runs back at Rarity house/thing we find out that they were there.
Yeah. Nice way to defend your friend, girls. Don't stick with her, just leave her to be expelled and throw out of school NO, just leave her and don't even try to make up things to defend her.
YOU FUCKING IDIOTS!

Here is something easier.

2207624 I totally disagree with the second one where it says that the movie is enjoyable, cause it is NOT !

2158172 That's not a plothole or convenience though.

2294363 I've got a new convenience: In this alternate universe highschool there are the Human version of the Mane 5, princess Luna and Celestia, the CMC (and so even the family of Applejack and Rarity), Cherrylee, Trixie and other characters, but there is no trace of the Human Sunset Shimmer and neither of Twilight Sparkle? Rrright
And a possible plot-hole: shouldn't Sunset be older of Twilight? "The Fall of Sunset Shimmer" showed that Sunset had the same age of the main series and Twilight was still at the same age of the CMC. Following this things, shouldn't Sunset be at least 10 years older than TS?
And a mix of plot-hole and convenience: Alicorns Princess Celestia and Luna are immortal, but the human is not. So, it just happen that Twilight arrival in the Highschool just when Human Celestia and Luna were there?