The problem with most of X-villains they kinda become expendable after few story arcs, that's how Apocalypse and Juggernaut were introduced as unstoppable forces, were reduced into jobbers. The whole countless reformed-and-back is also a notable factor, but I still find many X-villain ideas to great, with potential for immense stories:
Magneto - he isn't just a villain to your heroes, he is an ultimate nemesis to almost everybody who stands between him and his cause, both villains and heroes. And these reasons might sound righteous and just, but achieved in most ruthless and objectionable ways. He already damned his soul time and time again, and accepts this as a price he must pay to give his people an opportunity to raise their children the way his parents never could (too bad most of his achievements resulted in even bigger tragedies for him and his people)
Sinister - he was there at Darwin's funeral, he was there in Nazi cc's, he was there in Vietnam, he was there at Weapon X facilities, he was there for most of the X-life to insure, in most of manipulative ways, his final goal - to design a perfect godlike genetic creation (if only writers could make him realize there's already one - Franklin)
Apocalypse - ancient powerful mutant, one of the really first ones, tasked by the Space Gods themselves to become a caretaker of evolution on Earth, with tech beyond human comprehension. The whole concept of his goals are so fundamental it actually makes X-struggles look so small from the universal order perspective (still looking forward for more prehistoric interactions with Inhumans, Eternals and Pantheons, especially the Egyptian)
Exodus - an immortal powerhouse, his origins start during Crusades and him being the man that wanted more and reached for that opportunity finding Apocalypse, who eventually turned him into Exodus we know. Then continued with him as Magneto's high ranking enforcer - too bad he never had anything of a stable character development afterwards, but I like that he wasn't always portrayed as purely one-dimensional supremacist (giving him stable will, depth and reason could turn him into someone resembling what Magneto once was, as similar Crusades continue nowadays as well)
Joseph - now this one Magneto: NAH made me realize how potentially perfect Magneto nemesis he actually is because - he is Magneto. Except Joseph is young, powerful, ruthless and has no trauma that could actually hold him back or drive him into madness, lack or sufficiency of which for most part are always the factors for Magneto's past defeats.
Vulcan - I don't understand all the hate he receives, he has everything good character needs: tragic and interesting background, incredible powerset to potentially manipulate 4 fundamental forces, 7 elements, kinetic energy and was already shown to be able to play with magic energies (Beyond Omega-level energy manipulator), AND is a third Summers brother!
What was kinda disappointing is that he was portrayed too one-dimensional, but that can be explained as something his powers and bloodlust were to blame as any capable writer decides he wants to use him (Omega Summers and Sinister is not interested? How?)
Juggernaut - like the idea of a non-mutant X-villains, but I find Marko pretty boring, so I don't mind the Juggernaut mantle being wielded by another character, idea Gillen already established. I can even see how Cyttorak might develop some X-obsession after everything that happened between them.
Sabretooth and Mystique - street-level, black markets and assassination shenanigans, that's where I see them. And not just sociopaths with anti-X-men/Wolverine obsession. Actual goals, even the recent Mandripoor thing can be good if done rightly.
Nimrods/Bastion/Omega Sentinels - more A.I. against mutants. Make the Sentinels evolve into some kind of more interesting self-driven force overgrowing human robot-slaves angle and it would be just perfect.
Hellfire Club - not the Sh!tfire Brats, but an actual Club, I want them more behind the scenes with an actual influence/authority-driven agenda, manipulations and shenanigans on the highest ranks and of course a credible lineup, like in good old times.
Selene - she is the first mutant, nuff said.
Purifiers - they just need more interesting ways of eliminating the mutant threat, like high-tech battle suits, super soldiers/mutates and also more charismatic characters.
High Evolutionary - I don't know how much he is considered an X-villain, but for me he is sure one of the best ones. His quest kinda resembles Sinister's (for obvious reasons) yet he isn't 100% amoral and fanatic, and in this cold reason conceals the same aspect that makes a great villain.
Honorable mention: Mikhail Rasputin - just for the vast potential :)
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