"Elements are tied to their personalities! And if that changes badly enough thanks to their Cutie-Mark-change-induced-personality-alteration, the Elements of Harmony might became confused and deactivate, leaving this realm defenseless against future forces of Disharmony that might seek to destroy it!"
"Then we have no choice. Much as we regret it, the needs of many outweighs the needs of few. We have to change them back, NOW."
And what if it doesn't work that way? What if NOT changing back would have CATASTROPHIC consequences even if they liked their new lives and the others respected that? What if the universe doesn't offer them a real choice?
That still wouldn't make them good at their tasks. And if they could learn how to carry them out, imagine how long it would take for them to fix the chaos they caused. Seriously, it was like Discord went loose all over again, only this time he didn't have to lift a finger.
When you think about it, each of Twilight's friends switched cutie marks (but not talents or personalities) with the friends they're the LEAST like, and were made to believe they earned their cutie marks doing things they're the least suited for: Rarity is too refined to handle weather like the wild Rainbow Dash, who's too rough to care for animals like the gentle Fluttershy, who's too quiet to host parties like the outgoing Pinkie Pie, who's too scatterbrained to do hard work like the organized Applejack, who's too uncouth to make dresses like the elegant Rarity.
Much of the show is about being oneself and not having to change who you are for the sake of anyone else. This is present all the way in the series premiere, where Twilight's friends help save the day simply by being true to themselves. The events of "Magical Mystery Cure" allow Twilight to finally return the favor by guiding her friends to be themselves once more, rather than have them keep forcing themselves to be what they're not. After all, a true, true friend helps a friend in need.
Now, that's not to say someone can't write a story like the one you suggest. God knows not everyone feels the same way about "Magical Mystery Cure" as I do. One could argue that Twilight wouldn't be forcing her friends to make the best of their situations, as hard as that may be. I do believe one can achieve happiness by overcoming obstacles, even if those obstacles may seem impassable. But that's not why I think the show is so wonderful, and it's for this reason that I love "Magical Mystery Cure" for what it is: a celebration of the characters who helped make MLP what it is.
(I dare not take all the credit for this mini-essay. Much is drawn from this editorial that helped blow my own uncertainties of the episode away: www.roundstable.com/2013/02/21...
Ok I look at this a second time and all I can think is of a line from the fanfic Growing Pains, where after hearing Applejack read the label of a mane conditioner bottle in a /very/ sultry voice, the only thing Rarity can say to her is "DO THE SEXY VOICE AGAIN! IT MADE ME TINGLE IN PLACES I DIDN'T KNOW EXISTED!"