I like Twilight Sparkle, and don't really see how she can be a Mary Sue. Protagonist, sure, but the only episode where she seemed really "Sueish" was Magical Mystery Cure. Otherwise, she isn't a blatant self insert of either the writers or Tara Strong. Heck she isn't anywhere remotely like Tara. She isn't considered beautiful, but more importantly she isn't considered *remarkable* in appearance, at most she's described as a little scrawny. She has an ordinary eye color (for a pony) and she's a terrible dancer.
I'm just reading through this and trying to figure out where people would think of her like a Mary Sue: http://katfeete.net/writing/sue.php
Princess Mi Amore Cadenza is off the charts, but Twilight barely registers. Even Applejack gets a higher score, what with the dead parents, and the freckles, and winning an award for being the most well liked pony in all of Ponyville.
There aren't any prophecies about Twilight, specifically. There are ones about the main 6, but the prophecy stuff cuts off pretty much once Twi gets princess'd. I mean, I guess she's royalty now, but she was born to just ordinary parents, who weren't abusive or anything. She's also taking a more passive, supportive role in the background as a princess, and going absolutely nuts for not being able to participate in any of the adventure.
Not everybody likes Twilight. Heck, Sparkler hates her guts for one-upping her organizational skills. Twilight even aggravates her friends at times, though less so as a pretty princess. She doesn't rage against the machine, and is pretty content with the way the world is.
Any character can be portrayed as a Mary Sue, but for all Twilight is ridiculously overpowered at times, I just don't see her fitting in that role most of the time.