Well, Meredith in Dragon Age 2 was a good female villain/antagonist in the sense that she wasn't sexualised, (you get no boob armour), she is a very physical fighter (I think it was a very concious choice to make the leader of the less physical mages a man and the templar knight a woman) and an older woman too.
All things we don't see as much as I'd like.
Her writing had issues, but none of those had anything to do with her gender.
Batou667 said:
No, there aren't very many female antagonists - because blowing away dozens of faceless men is business as usual, but society isn't ready to see women made as expendable, it seems.
It's not like those men are seen as expendable for their masculinity either.
Since those faceless grunts are generally blown away by male protagonists.
It relates back to the whole idea of men being the norm for most things.
Make a character (a standard enemy or a protagonist) a man, and it's business as usual.
Make them a woman, and it's suddenly a 'message'.
The only way we can get away from this idea is to have more even splits in all roles; more female protagonists and more female background characters and enemies.