I think it's time to take the phrase "Mary Sue" back, and this is what I'm trying to do with the Mary Sue Virus. It is a blatant SI but... from what I've been told, it is well written and a good story. Granted these Sues are well aware of what they are and what they are doing, and maybe that's the secret. If Mary sue is aware that she is annoying and perfect and powerful, but she has a distaste for that, and tries not to be that stereotype.
Now that that's out of the way, the typical bad "Mary Sue" is annoying and perfect and loved, and well, that's just not interesting to read.