Prepare for a lot of conjecture!
Already a few members have mentioned that this episode had the feeling of My Little Pony: Friendship Is Magic's denouement. Before the season even began, back when Season 3 was announced for 13 episodes, a lot of fans were speculating that this would be the end. Perhaps such was the case when Season 2 was wrapping up production and Season 3 was under development. I could easily imagine "Magical Mystery Cure" being the capstone episode for the entire series. With 65 episodes in the bank, The Hub could have reruns of MLP while focusing on new franchises (i.e., Littlest Pet Shop).
Consider that the central thrust of the season was confronting one's destiny and finding the strength through friendship to overcome obstacles. This was MLP's destiny at heart. And to have Twilight become a princess---a move which sounds more like a Hasbro dictate than the designs of Lauren Faust and her successors---is the ultimate climax and "resolution" for the pervasive themes of friendship and magic. Twilight ascends to a princess; it sounds just plausible enough with some in-universe explanations to have been the plan from the beginning---I am not so convinced, however. I am under the growing impression that DHX Media had the initial orders---probably at the start of Season 2's run---to conclude the series with a bang that did not completely close the door on the story. Younger kids would then be less inclined to view MLP as having ended in lieu of the quasi-cliffhanger. Cue Princess Twilight product placement filling the void.
I wonder now if this was one of the reasons why Lauren Faust decided to leave MLP after the first two seasons. (She stepped down as showrunner after Season 1; she remained listed as an executive producer until the beginning of Season 3). I could imagine her being opposed to the idea of making Twilight a princess, potentially spoiling one of the central themes of the show, i.e., they are "normal" girls capable of amazing things. Princess Twilight radically alters the playing field. She is technically her friends' superior. It's even difficult to describe Twilight as the first among equals. One can say that Princess Twilight is the unofficial severing of ties with Lauren's initial vision, because I do not have the impression she had this in mind from the start. I hope that one day she can address the matter of Princess Twilight Sparkle. Whether I'm proven right, wrong, or a little bit of both, I'd be interested to hear her thoughts.
The essence of "Magical Mystery Cure" as originally designed to be the series finale can be viewed in the final five minutes of the episode. Twilight is transported into an astral plane, where Celestia personally shows her through brief montages of events from previous episodes. How could that not be the end? The montages had "Thanks for watching!" written all over it! The subsequent shift to the coronation, the callbacks and references (e.g., Celestia referring to her reunion with Luna), and the triumphant ending only reinforce that message. It's not unlike seeing your life flash before your eyes when you are about to die.
Bronies, I think we just had a near-death experience.
I am going to assume that MLP's popularity explosion (the ratings don't lie), undoubtedly fueled by the Brony phenomenon, led Hasbro to have second thoughts once Season 2 concluded. They were sitting on a veritable gold mine. Recent shifts had occurred in their marketing scheme, from gradual improvements to their MLP: FiM merchandise to advertising more aggressively geared toward older audiences, which seemingly confirm that Hasbro is taking MLP: FiM more seriously than they had when it was still aimed exclusively at young girls. Without Bronies to propel the ratings, I suspect we would be waxing poetic about how MLP had meant so much to us over the past three years, and that we were said to see it end.
The byproducts of Hasbro's decision---and I am still working under my presumptions of a near cancellation---are readily seen in both Season 3 and its finale. Within the truncated timetable, the writers were attempting to hit a lot of high points. The results were mixed, I think, due to the relatively short length of the season. Many of the episodes were arguably better suited for two-parters (i.e., "Magic Duel", "Keep Calm and Flutter On", "Games Pony Play", and "Magical Mystery Cure"). If Meghan McCarthy's recent comments are any indication, Season 4 will rectify this issue off the bat. The debut episodes will very likely tie directly into the events of "Magical Mystery Cure"---or, in lieu of the three-part continuity, "Twilicorn Begins".
(Five paragraphs before a Christopher Nolan Batman reference! A new record for Season 3! But don't get on my case: all this talk of "destiny" and "ascension" was bound to have Ducard lurking somewhere nearby, asking if Twilight was truly prepared to do what was necessary.)
So, after all of that rambling, what did I actually think of the episode? As I alluded to before, this would have been a terrific episode for a two-parter. M.A. Larson nonetheless did a wonderful job of condensing an otherwise complicated premise into short bursts of exposition. Twilight's "I accidentally defied the laws of nature last night" explanation still leaves a lot to be desired; but I don't hold that against Larson so much as I do the constraints in which the episode was created. By turning MLP into a musical for an episode, Larson kept the pacing smooth while still elaborating on the central conflict. By and large it was a real triumph of writing talent that "Magical Mystery Cure" managed to pack so much content into 22 minutes.
I'll be the first to admit that the unfolding of Twilight's ascension surprised me. Let me be clear: I didn't scream, "Oh, my God! Friendship is the key! I can't believe it!" I did, however, predict that Twilight was going to switch destinies with one of the princesses; but that was a matter of the initial descriptions being unclear as to how expansive the destiny swaps would be. I also remained incredulous that the princess fix was going to be long-term: my prediction was that once Twilight fixed everything, she would return to being a normal unicorn. That obviously did not happen. I'm not distressed, though: I have faith in the writers that they will handle the matter deftly.
(I am disappointed, however, that the litany of Chekhov's guns were effectively ignored---the Alicorn Amulet being the most prominent of them. Only Starswirl's book returned to the forefront. It didn't feel as though the inclusion of new magic and artifacts truly came full circle. Maybe that will be handled in Season 4? I sure hope so. It would be disappointing for the sudden dangers of Equestria to be conveniently ignored.)
The best scene of the episode was when Twilight and Celestia met in the astral plane, just after Twilight got zapped by her friends. Celestia at last received a singing role! How awesome was that? Nicole Oliver has a wonderful voice; I'm glad they took full advantage of it. Combined with the montages, the whole scene was moving. If this had been the series finale, I probably would have begun to sniffle---shedding some liquid pride, as Shining Armor might say. The entire sequence was very well done.
Oh, and what do I think specifically of Princess Twilight Sparkle, the newest Alicorn of the bunch? First of all, I wasn't terribly distressed by the news in the first place; second, what good what it do me to get annoyed over the change? Why drag my feet and pretend it didn't happen? I like it. I'm willing to give it a try. If it backfires... well, them's the bricks. I happen to believe the concept has a ton of potential.
In terms of overall quality, "Magical Mystery Cure" was a strong episode. I hesitate to place it in my top three due to the time constraints which weakened what could have been a truly momentous two-part episode. I am still of the mind that "A Canterlot Wedding" is MLP's magnum opus. Everything that is great about the series can be found in that episode(s). That having been said, you now know which season finale I think is the best.
Another point of weakness for "Magical Mystery Cure" may have been the hype. The conflict meant little since it was long since established that it was simply a set up for Princess Twilight. "A Canterlot Wedding" kept me guessing and invested in the entire narrative; "Magical Mystery Cure" was all about Princess Twilight Sparkle, the Alicorn. Everything else had become a formality. The tension existed solely in the end result rather than the process by which we, the audience, arrived at the end. I wish it could have turned out differently in this regard, but I doubt much could have been done to avoid the rabid obsession with Twilight's transformation.
With all this digital ink having been spilled, my abridged assessment is this: "Magical Mystery Cure" is the epitome of Season 3. Season 3 was far too brief. I do not mean this simply in terms of desiring more ponies: a lot of information got crunched into compact elaborations. Never did the full string of events unfurl themselves, even after the numerous allusions. Though such was the case, the experience in general was a great deal of fun.
I am eager to see the next chapter in this fantastic series!