A lot of the problem with Magneto is the attempts to handwave his earlier stories, and handwave the fact that he is the main reason mutants are hated and feared. They've tried to retcon him into being a necessary response to how mutants were treated, and it doesn't work in the context of a time when there were less than 30 known mutants.
Claremont wanted to end his run with Magneto fully redeemed, accepted as a hero and the new leader of the X-Men after Xavier dies, and a lot of the fans agreed with him, but he never created a new villain worthy of replacing Magneto as the X-Men's archenemy, so other writers wanted him to be a villain again, adaptations and marketing all wanted him to be a villain, leading to the 1990s after Claremont, where he retained the backstory which explained his position, but he was a villain and the X-Men had to protect the world from him, his followers and his ideology.>>117987985
Magneto keeps reeeeeing about Hitler but is always on the brink of becoming as bad as him, or worse, was a constant theme, and Morrison actually followed through on it, and everyone lost their minds, it was one of the only stories Marvel immediately retconned as soon as there was a change of writer. Magneto's been an ally or member of the X-Men ever since because that's what the X-fags want, and what the moviefags want.
Cullen Bunn wrote Magneto's solo book, then wrote him in Uncanny X-Men and X-Men Blue, spending six years moving him back to the red costume, Asteroid M, the Brotherhood, and fighting against the X-Men, even /co/ screeched about regression and undoing character development. As soon as his run ended, Marvel ignored it and put Magneto back with the X-Men. I don't know how we ever go back from this now.