The third season finale of My Little Pony: Friendship is Magic, Magical Mystery Cure, should not have been able to happen in the way that it did. There was way too much in it that didn't make sense. Now, you might be saying "But magic!"

Well, sure. Magic. But that's actually a major part of the issue with the episode.

Because Magic A should be Magic A. The Friendship is Magic 'verse has, in the sixty-four previous episodes, built up a somewhat solid ruleset for how things actually work.

The entire problem with Magical Mystery Cure (from here on referred to only as "MMC") is that it breaks those rules. The only prior occasion when the rules were flagrantly broken involved Discord, a character who is an embodiment of chaos and specifically capable of breaking those rules. When Discord was around, it was obvious the rules were being broken. MMC broke the rules in a much more subtle manner, something that makes me personally suspect that it was originally meant to actually involve Discord - but I digress. Let's look at what the episode actually did.

First off, there's the whole business with the cutie marks. From the earlier episodes, specifically "Cutie Mark Chronicles" and "The Cutie Pox", we have a fairly good understanding of how cutie marks work. A pony recieves his or her cutie mark when they realize their special talent. Not necessarily what they want to do with their lives - but their special talent. Often, the design of the cutie mark can be somewhat esoteric in its relation to the talent, but a cutie mark does not decide what a pony has to do. Instead, it notes something a pony have a special affinity for, something that they can then incorporate in their life goal. In some cases, it's a fairly simple equation - most obviously with Applejack. On the other side of the scale, you have Rainbow Dash, but perhaps most interestingly for this analysis, Rarity. From Cutie Mark Chronicles, we know that Rarity's talent isn't directly related to dressmaking - she was interested in that before she got her cutie mark, and would have continued down that path incorporating her special talent into it no matter what her talent/cutie mark actually turned out to be. Her special talent is directly related to gems, not clothes. Remember this. It will be important later. Additionally, from The Cutie Pox, we can see that the talent/cutie mark relationship goes both ways - when Apple Bloom gets her magically artificial cutie marks, she immediately gains the related talent. Add to this how the cutie mark crusaders go about trying to get their cutie marks - they try to find their special talents. They don't try to find what they want to do with their lives. So, bottom line here - cutie mark/special talent and (for lack of a better term) way of life are two distinct things. In pony society, a vast majority of the population will shape their way of life around their talent, but there's no direct relationship.

Now consider how Rarity acts the first time we see her in MMC. She has Rainbow Dash's cutie mark and is trying to control the weather. She's trying to do Rainbow's job. This makes no sense. Important to note here is that Rarity doesn't actually think she is Rainbow Dash - she merely thinks she has to do what Rainbow Dash usually does. But if we're supposed to think that this is due to her having gained Rainbow's cutie mark, this is where the entire plot crumbles. Rainbow Dash is a pegasus. Pegasi have their innate magic relating to clouds and weather. Rainbow Dash would be on weather duty no matter what her cutie mark was, and Rarity doesn't think she's Rainbow Dash - or even a pegasus at all. Instead, Rarity getting Rainbow's cutie mark should have meant that she now had Rainbow's special talent, which is... fuck if I know what it is, but from watching Cutie Mark Chronicles, we can be sure it has nothing to do with weather, even if the mark is a cloud with a rainbow bolt. Presumably it refers to being "fast as lightning". But since it's only special talents and cutie marks that go hand in hand, and that concept being distinct from what the pony actually does with their life, means that Rarity should only have lost her affinity for gems and gained an affinity for speed - and thus, the result should have been that she would still work with clothes, but with a different spin. Perhaps sportswear, or being the world's fastest dressmaker. She still knows she's Rarity the unicorn.

It follows suit with the others. Rainbow Dash should have gained an affinity for animals, Pinkie Pie an affinity for apples and Fluttershy an affinity for parties. Now, these are the things they actually tried to do in the episode, and they were just bad at it, so you could argue the point about them - but it's when we get to Applejack getting Rarity's cutie mark that everything falls apart again, because Applejack tries to make dresses. Remember: Rarity's talent has nothing at all to do with dresses. Applejack didn't try to do anything that involved gems. She just made bad dresses.

Conclusion one: The cutie mark swapping should have had vastly different effects.

Now, let's look at the event that actually caused the cutie mark shuffling - the spell that Twilight cast, which made the elements of harmony go nuts. And this is where they throw even more rules out the window, because from previous episodes - "Elements of Harmony", "Return of Harmony" and "Keep Calm and Flutter On" - we have an understanding of how the elements actually work, too. They're not just magical powerup artifacts. They're a set of magical artifacts that only when used in conjunction with each other, in harmony, wielded by the ponies that embody the six elements, confer any actual power, and this power has so far always taken the same form, which I'm going to call the rainbow of light because it's an obvious reference to it from the old My Little Pony show. So, the elements are magic, kindness, loyalty, laughter, honesty and generosity. Compare these to the cutie marks/talents of the wielders - magic, animals, speed, fun, apples and gems. Note how not all of these line up with the elements? Magic, obviously. Laughter and fun, of course. Kindness and animals could be argued, but the other three don't have anything in common, especially when you look at how Rarity generally is not generous with her gems. So we can easily see that the elements of harmony are completely distinct from the talents of their wielders. Presumably, the elements attune themselves to the pony that use them for the first time in each "generation" of the elements... but this still does not in any way equate them with their talents. If anything, the shuffling of the elements should have shuffled the... well, the personalities (not the best term, but work with me here) of the element holders. It should not have touched the cutie marks. Rarity should have instead lost her streak of generosity and have become increasingly loyal. Pinkie Pie should have become as reliable as Applejack used to be.

To sum that up, we have three distinct things here. Cutie marks/talents, interests/ways of life, personalities/elements. MMC conflates all of these into one, which goes against just about everything we have learned about them. In light of this, the way they were restored was somewhat sketchy as well. Were they reminded of their talents? Their interests? Were their elements forced back into them? Looking at what happened makes none of these make any fucking sort of sense at all. So the entire business about the shuffled cutie marks shouldn't have worked at any part of the plot, unless Discord had something to do with it. And if the episode had, as I now suspect, been entirely about the cutie mark issue, then it being Discord fooling around again would have been my guess for conclusion of the plot. Apparently we have two more episodes of the plot to go - but right now, it's a trainwreck of everything.

Conclusion two: The cutie mark swapping literally can't have happened like that.

But o ho ho, we're not done yet. No, we have the other controversy of the episode left to dissect - Twilight becoming an alicorn.

Luckily, we know things about alicorns too! Specifically, we know that they're the top tier beings of the 'verse. Ponies with insanely powerful magic. We have three of 'em - Celestia and Luna are physical gods who are literally in command of time and space and have reign over celestial bodies, and Cadance, while not as powerful as Celestia and Luna, is straight up pony cupid (and if we want to assume further, she can manipulate love). This is personal theorycrafting again, but I'm finding it likely that Discord, before he became a Draconequus, was an alicorn as well, presumably with an affinity for chaos magic and this is eventually what caused him to go insane. So we know that alicorns are incredibly powerful. Celestia and Luna are centuries old, and we don't know if they were born alicorns - but they probably were. They have, very clearly, stopped aging. Celestia is definitely the most powerful being in the 'verse, and Luna was on par with her before she got imprisoned. From Twilight's flashbacks in "A Canterlot Wedding", we definitely know that Cadance is still aging at the rate of a normal pony - she seems to be a little older than present time Twilight in the flashbacks. With how she just got married and all she probably isn't going to look forwards to seeing Shining Armour getting old and dying while she just kind of stops aging. Cadance is not a physical god, and I cannot imagine she was not born an alicorn. Luckily, another episode gives us some insight into pony genetics - "Baby Cakes", which shows that two earth ponies can have pegasus and unicorn children. Pony genetics run deep, meaning that it's very likely that somewhere up Cadance's family tree, there was probably an alicorn. Perhaps even Celestia herself, hundreds of years ago. Whatever the case, there's nothing that points towards that it's possible for anyone to become an alicorn after the fact. Even if you could, it's been conclusively shown that alicorns wield epic-level magic.

But here's the thing. We know that Twilight does not have magic anywhere near this level.

Twilight's special talent is magic. This does not imply she has incredibly powerful magic - let's call this quality of magic. What we have seen is that she has been able to learn many new spells, something other unicorns haven't been shown to do - which I'm going to call that her talent is that she has a very high quantity of magic (a high quality would make it easy to get a high quantity - but the other way around does not appear to be true). We only have to go back eight episodes to get the proof, to "Magic Duel". The alicorn amulet artificially confers to Trixie a vastly improved quality of magic, but not entirely physical god levels. She, while wearing the amulet, seems to be at a power level stronger than Cadance, but definitely not anywhere near the level of Celestia and Luna - it doesn't give Trixie alicorn magic, it just boosts her own magic to the extreme. She is capable of casting very powerful spells, and it's implied the most powerful of the repertoire she displays is weather spells and age spells - stuff that would probably be cantrips for Celestia. When Twilight returns for the second duel, to one-up Trixie, she gives the impression of easily casting a series of age spells, and upping the ante with a duplication spell and a gender spell. Trixie comments that nopony can do those spells.

Twilight replies with a confirmation. "Not even me."

The entire aesop of the episode revolves around that Twilight can't do that level of magic on her own. She had to rely on the assistance of her friends to do it - "A different kind of magic", indeed. The elements of harmony would probably have been able to counter the alicorn amulet and disarm Trixie, but they would not have allowed Twilight to actually cast those spells.

Now, we don't actually know how much time has passed between Magic Duel and MMC, but it really doesn't seem to be a lot. We have some clues on how much time has passed from the beginning of the show, and it can't be more than about a year. Whatever the case, there's simply no possible way for Twilight's magic to have improved that much since Magic Duel.

Conclusion three: Twilight doesn't have alicorn-level magic.

So let's put those things together.

1) The effects of the cutie mark swapping can't have happened.
2) The cutie mark swapping can't have happened.
3) Twilight's alicornization can't have happened.

Final conclusion: Magical Mystery Cure can't have happened. It breaks too many things established throughout the previous sixty-four episodes. It breaks the entire 'verse. Only two characters have shown the capability to do that before: One is a being who follows no rules of anything ever and breaks whatever there is to break purely for amusement, and the other is Discord.