In my opinion, the dreaded Mary Sue is more feared than she should be. I am certainly not denying her existence. Most fandoms have their share of unfeasibly-accomplished young girls who come in out of the blue to (to use SGA examples) trounce McKay at science, best Ronon at fighting, and cause Sheppard to become a marvel of emotional openness as he gushes of his undying love for her. I am not for one moment saying that this is a good thing. Fictional characters should always feel like real, rounded humans, and the super-accomplished flawless Mary Sue character doesn't.
However, I believe that the Mary-Sue menace has been over-stated. I've several times read people say, "Oh, I never read any story featuring original characters, since I know they'll be Mary-Sues." Now, I'm sure that all fanfic readers, especially in large fandoms, pass over many stories, judging them by their summary to be something they don't want to read, so people have every right to say things like this. They also have every right to say, "I'm in fanfic to read about the canon characters I love, and don't want original characters cluttering it up." Fair enough. I just think it's a shame that it's come to this: that the default for an original character is seen as a Mary-Sue.
I feel that it encourages readers to cry "Mary Sue" unjustly, and that it limits writers. A few years ago, a friend rather half-heartedly recommended a novel to me. "It's okay," she said, "but the heroine's something of a Mary Sue." I read the book, and I really didn't see where on earth she was coming from. I felt that the heroine was a well-rounded, very human character. Yes, she was feisty and accomplished, but not unfeasibly so, and there were many other facets to her character. My friend, I felt, had seen "female," "feisty", and "accomplished" and concluded "Mary Sue." (In this case, the hero was a veritable paragon, and the author was clearly head over heels in love with him, but that drew no criticism from my friend.) But what was the alternative? Had the character been a little less feisty and a little less accomplished, my friend would doubtless have denounced the novel for having a bland, wilting non-entity of a heroine.
The risk of this, I feel, is that authors will be so scared of writing a Mary Sue that they go too far the other way, and create characters that are either a laughable bundle contrived flaws, or are just bland and weak. ("Accomplished female = Mary-Sue, so let's not give her any accomplishments.") People often lament to lack of well-written female characters in science fiction and fantasy and also in fanfic as a whole. I'm sure there are lots of reasons for this – I , for example, favour male characters in fantasy for purely shallow reasons: because I like to fall in love with them – but could it be that the Mary-Sue issue has something to do with it? Could it be that some authors are scared of writing interesting female characters because they're afraid they're going to be accused of writing a Mary Sue?
I can attest to at least something of this. I'm currently writing a long original character outsider viewpoint fanfic, and both my main viewpoints are male. There were several reasons for this choice, but one of them was definitely the knowledge that some readers would see "original female character" and would automatically assume a Mary Sue, and read no further. With original male characters, I felt, people might at least give it the benefit of the doubt.
I just think this is a shame. Mary Sue exists, and I'm certainly not saying that she's a good thing, but I don't think she exists half so much as some people think, and I think that the constant talk of her can be rather damaging. I think that original characters should be seen as not Mary Sue, until proved otherwise,