I don't get what everyone finds so confusing about Magical Mystery Cure. Twilight has "graduated" from her current level of studies and is now going to take a different path. Most episodes are slice of life style so the major plot driving ones can seem out of place sometimes. Usually these types of episodes are two-parters and this one needed to be. The pacing was off, but enough is there as needs to be to make minimum sense. Remember: MLP doesn't make total sense in the first place when you think about it that hard. Put away the microscope and enjoy the ponies.
Your comparison is not very good and you're trying to have it both ways. You're alluding that the bronies who threw a hissy fit over Princess Twilight are NOT whining fanboys, but the gamers who spent hundreds of dollars and invested hundreds of hours of time, who were promised something (THAT THEY PAID FOR) that they did not get, are just whiners. Also, the ending was not changed, it was extended and still has massive plot problems and is a giant let down. Just because the industry controlled gaming media rushed to Bioware's defense, doesn't make it true that the fans are jerks. And gaming is an art form, nobody is trying to stop that, nobody can, because it already has been one. Artistic license and bad writing are two hugely different things. See the Star Wars prequels for an example. And, do you really think that the FiM team is going to go with a story arc that ruins the lives of Twilight and her friends? All we know is that Twilight has gone to the next level, things are going to change and tune in this winter to see how.
My Little Shinigami: Shounen is Magic would be AWESOME!
But like I said before, nobody will be left behind, nobody will be left to die, that's not what the show is about and there is no way the actual writing team will do this. Also, what's wrong with a mild Mary Sue? Most characters in most stories are to a certain extent, which is why I hate how the term has expanded to basically include all fictional characters and is thrown around constantly. Twilight isn't soloing Cell or anything, just because she's an alicorn now. Celestia, the deus ex equus (god in the horse ) couldn't even defeat, well, basically anyone on her own. Even in flashbacks she only defeated old enemies with her sister and the elements of harmony. If even Celestia needs help to do stuff, then Twilight, who is nowhere near as powerful, needs all of her friends. So, I wouldn't worry about any of your concerns coming true.
Hopefully this didn't come across as hostile, not intended to be. Don't worry so much about season 4 it'll be great!