Bronycurious (or Tommy Oliver now) tossed up a surprisingly interesting analysis on Mary Sue as a whole. It primarily compares Twilight Sparkle to Superman, and the two of them against a blatant fanfiction style epic mary sue. As with all anlysis, the subject matter can probably be debated to the moon and back, but that is kind of the fun of it.
Anyway, go get it below. What are your thoughts on Princess Twilight's sue status?