As far as I know, the definition of a "Mary Sue" is a character that is conspicuously without flaw, or has informed flaws that hold no regard to thier capabilities.
I have only seen two characters that actually fit this, despite the internet's insistence that they're all over the place. The first is Tyber Zaan, and I don't think I need to explain that to you. The other is Yotohime . . . something, in one of the Touhou mangas, who basically exists purely to beat the series herione and a few of her friends, while somehow looking like she should lose anyway.
I've seen a lot of characters accused of being Mary Sues when other terms apply better. If you will pardon me using Tv Tropes terms, Flanderization is the term I think would apply better to Mara Jade and Thrawn.
Currently listening to: Sand Dream
Currently working on RPGMaker