I'm not sure I buy the Mary Sue argument about Twilight. Sure, she's gotten powerful, and she got to be a princess, too, with all the perks and responsibilities that came with that. But that's not the entire story of her. She's visibly chafing at the princess thing for one.
Take this episode, for instance, she gets to sit in the royal lounge with the other princesses, but how does Twilight see it? She doesn't get to sit with her friends. She does what she has to... because Twilight is that kind of pony, but she'd much rather be down there freaking out over medal counts with Pinkie. But, duty calls, and Twilight, as always, responds. Whether she wants to or not.
I kind of hope that this becomes something, at some point. There's apparently one lesson in friendship that Twilight is still lacking... and that's saying no. To Princess Celestia, in particular. I mean, sure, Celestia's requests usually come down to Saving the World, or similar, but still... I do hope there's a big solid "No!" coming up at some point. If they're supposed to stop being Master/Student, somepony has to break that old bond so they can build a new one. And it will hurt. But... Twilight will have to do it at some point if she wants to become her own mare, princess and all. Unless she's happy being groomed into somepony she's not.