The word "villain" didn't even register for me from the original post. Villainy in comics doesn't exist in the same way as it used to. And when we liken it to Magneto, Marvel has been a Magneto Apologist for more than 40 years. So when we look for a "Magneto" style "Villain", I think Anti-Hero Extremist. Not villain.
If you're looking for villainy, the only true villain we have left is Sinister. Marvel is even an Apocalypse Apologist at this point. Sinister's the only one, but his mission is WAY WAY too selfish to represent mutantkind at large.