Well the good thing about the X-Men Franchise is although there have been no main female villains there have been lots of secondary female villains; Mystique (
) Deathstrike, Phoenix, Calisto, Arclight, Emma Frost, Angel Salvadore & Viper.
On the MS front they have Maya Hansen and the Extremis woman
Magneto: Does it ever wake you in the middle of the night? The feeling that one day they will pass that foolish law or one just like it, and come for you? And your children?
Professor Xavier: It does, indeed.
Magneto: What do you do, when you wake up to that?
Professor Xavier: I feel a great swell of pity for the poor fool who comes to that school... looking for trouble.