Well, let's see ...
I have Dr. Infanta, who is cute if she likes you but scary as fuck when crossed. Captain Right is half of Kraken's top leadership, and the one who does most of the facetime meetings because her other half hates to. The two of them have tremendous power.
Koroleva, the Chessmistress, is another powerful manipulator but hasn't appeared very often. Of course Farce has some of the highest screentime. Fortressa is fine with women but downright cruel to men, and not picky about whether they deserve that. Cacophony isn't interested in taking over the world, but she does have something that men don't like to see in women: a loud voice. Cold Shoulder is notable for responding to sexual assault by freezing most of Rabid City. I love Dvorak because she's such a fantastic foil for Qwerty -- they're like the bad older sister and good younger sister, only not actually related. And Dvorak is the more powerful of the two.
Not a lot of my series have major villains. A Conflagration of Dragons is, logically, split about half and half on the sex of the dragons eating their cities.
If you want more female villains, feel free to prompt for them.