My 2 cents on this discussion so far:
I don't agree with the "sexist" comment at all.
In a harem anime, even if the guy is completely useless, the girls still need to "earn" his affection: not because it is sexist, but because he is the only relevant guy.
It is not sexist since the same can apply to reverse harem: even the girl is nothing spectacular, the guys need to "earn" her affection just because she is the only relevant female.
As of the whole debate on Mary Sue characters:
I don't believe there is a way to say whether he/she is a sue character, as most main characters have some sue characteristics: whether it is too much or not depends on the audience personal tolerance. For example:
Spoiler for LOGH spoiler:
Yang Wenli is probably a 40/100 Stu: If you give him an army, he can achieve the best possible outcome; if not his opponent will act out of character just to let him win (Reinhard "climax" battle with Yang........why don't George Bush go to middle east with little guards to lure out the terrorist
). Thus I agree with Akito that in LOGH the best battles are the one Yang is not involved. However, the vast cast of LOGH and the interesting interaction of Yang and other characters make him not a stu: he may trivialize his opponents in battles (all his opponents in battle, including Reinhard, feels like a 3 year old when they face Yang), but not in the whole scheme of the story
I didn't watch SAO, so I have no idea what Kirito do. But given others comment he is probably a 60-80/100 Stu?
Here is a new example:
In short, no, i don't believe having a sue-ish character automatically make the story bad, same with most other types of characters: having a "realistic character" (character that you probably meet every day on the street) have problems as well: if he/she is so "realistic" why is the story center around him/her? That happen when people accuse XYZ show/character is bland; having a weak character also have problem: it make audience grind their teeth to see such useless person in action. IMO, it is all about the writings. Accusing Sue-ish character ruin a story is similar to people who claims winning a lottery ruin their lives: it is not the lottery (sue character) that ruin your life (the story), the sole fault lies with you (the writer/the story writing) alone.