I don't see the point of debating is Mary Sue bad or good...
I had read through the whole thread before I made this reply.
As I seen so far, I basically understand what most people's Mary Sue are. But I just don't understand, what's wrong to have a Mary Sue in a story?
A Mary Sue character will not make your story unattractive. The only thing that make your story unattractive will be your style of writing and story plot.
As I said in some previous post, my very first Pokemon fanfic has a Mary Sue-ish protagonist. But she was not Mary Sue from the beginning, she only develop this Mary Sue characteristic slowly as she journey through the world and gain experience as a trainer and an adult.
And also one more thing: ALL adventure fictions will have its story events center around the protagonists, and the protagonists will eventually become "perfect" as they continue their journey. So it technically means ALL adventure fiction protagonists are Mary Sue (or will become Mary Sue).