Seanan McGuire has made an excellent post about the misuse of the term Mary Sue. It really is an excellent post, thoughtful and insightful and calling out some issues that people really need to pay more attention to because they're those issues that just slide by insidiously, sucking all the while. Heaps of things about unconscious use of derogatory terms for female characters we just don't like, whereas we'd probably use more analytical/critical language to describe male characters we don't like. (The difference, really, between saying, “she's a bitch” and “he's unpleasant and condescending and I don't like him because of it”. We might mean the same thing, but the different language choice unconsciously reinforces certain gender dichotomies.)
So that stuff? That stuff I totally agree with and could not endorse more. But there's other stuff in there that I didn't agree with, so I'm going to ruminate a little on why no, actually, ( I believe Mary Sue is a bad thing )
Just as a PS: of course readers are more critical of female characters. Most media with a strong female protag is probably aimed at a female readership (women read more than men anyway), and women have always been – and possibly always will be – more critical of other women. I'm not saying it's not a problem and something women should be aware of and work to remedy, I'm just saying that it's there and we haven't fixed it yet.