Oh so it basically means self-instertion.
I don't see how this is a bad thing but ok.
That's not really a solid definition - generally a mary sue character is "perfect" to an insane degree. Pretty much every shonen anime protagonist is some form of mary sue.
Misaka as a character when the actual plotline isn't involved (like in slice-of-life filler episodes) is great, but she gets kind of annoying when it comes to the actual story. Not as bad as Touma, though, since she doesn't do the "Touma speech" as often.
The absolute worst mary sue characters that have completely ruined series are still Kira Yamato and Suzaku Kururugi.
Poll