It seems that every new mutant is joining the xmen right now and that there are more Xmen than actual mutants at times. So I wanted to get some thoughts/ideas for mutants who would be villians for the xmen.
I would make Quentin Quire a villian for sure.
I'd also have some Scientist maybe a cousin, brother, colleague or an abandoned/adopted child of Dr. Rao start to try to systematically eliminate mutants. Creating cyborgs and biological weapons even developing ways to enhance human abilities to combat mutants.
Elixir would be almost a Magneto type figure. Having his own island nation of followers both mutant and human. Offering health aid to other nations only if they comply with demands. Also have him in contact with Apocalyspe so that as one of his horsemen he could cause sickness and death.
A female mutant who has strong powers of suggestion and can possess/control men's minds. I'd call her Cleopatra.
Thats just a few off the top of my head.