Honestly, I wish there were MORE female enemies in games. I feel like a lot of games shy away from putting female enemies in precisely because of the idea that it's not okay to hit a girl, and that sort of conveys the idea that girls are not worthy foes, or something like that. XD I guess the argument could be made that putting female enemies in games encourages violence against women, but how is violence against women any worse than violence against men? Violence is violence.
Two games in particular come to mind: Yakuza and God Hand. Both have heavy focuses on beat-em-up combat, but Yakuza contains exactly one female enemy across the entirety of the first two games (I haven't played the third one; maybe it has more female enemies, I don't know), and she's part of a sidequest that actually involves her being a man in disguise and her brother being a woman in disguise. You fight them both, but the woman has a male sprite and the man has a female sprite. It's an extremely minor event that is easily bypassed and has no bearing on the rest of the game; I don't think the two characters even get names. The thing is, there ARE well-developed female characters in that series who would probably be very capable opponents, but you never actually get to fight them.
God Hand, on the other hand, has a pretty equal distribution of male and female enemies, and all of them are equally capable of kicking your ass. Of course, the women in God Hand tend to be scantily-clad and noticeably jiggly, and the protagonist gets a special "Spank" move that he can only use against them. So...on the one hand, there's definitely some female exploitation going on there, but on the other, I really appreciate that I'm allowed to beat the crap out of both women and men with the same wild abandon.
I guess what I'm getting at is, the theme of the game makes a difference in this regard. Yakuza is a fairly realistic and gritty game (comparatively speaking; let's just ignore the whole "punching tigers in the face" thing for the sake of this discussion) about...well, yakuza, and it makes sense that the women would be vastly outnumbered by the men. God Hand is a completely crazy, over-the-top parade of demon smackdowns, so pretty much anything goes.
As a slight tangent, what about females in fighting games? Does performing a vicious combo against, say, Chun Li make you feel any queasier than performing the same combo against, say, Dhalsim?