Commander Shephard is kind of a bad example don't you think? He's a player-created character, he can be as ugly or plain looking as you like. Also he's a military guy, so it would be pretty silly for him to be unfit.
Other than that though, I mostly agree. However, I think what irks women is that while men are only represented a certain way, they are represented in a much more positive way.
The men are always strong and powerful, generally handsome too but that isn't usually the main point. They normally have many good qualities in both personality and appearance, far more than the average person in real life.
Women always have big breasts.
What does that seem to say about gamers' opinions of women and men?
(Do note I'm not a woman or a feminist, so I could be wrong about this. It's just something I've noticed)