>>121127554In the 1980s, Magneto changed sides and joined the X-Men.
In the 2000s, the X-Men changed sides and joined Magneto.
Marvel kept escalating the threat level until the X-Men were radicalized, and embraced isolationist and ethno-nationalist ideologies instead of Xavier's integrationism, a lot of the fandom willingly went along with it. It's hard for them to not come across as villains when interacting with any other Marvel characters, no matter how retardedly high the stakes always are so that they can insist everything they do is necessary for their survival.
As for Emma, she never truly renounced her past as a villain, she just changed sides for self-preservation, and got some implausible retcons about how she did nothing wrong it was all Shaw's fault. Even when written as a heroine who cares about protecting her people and especially the children, she still openly believes mutants are better than humans and telepaths are better than other mutants. The X-Men's transition from being heroes for protecting everyone to being entirely about protecting mutants from humans does indeed take place around the same time she moved from Generation X to the main team.