At the close of X-Men: Apocalypse, we see Jennifer Lawrence's Mystique leading a new team of X-Men in a Danger Room training session. That's right, not only is Mystique, a traditional villain, a member of the X-Men, she's the leader of the team. Director Bryan Singer acknowledges that doesn't align with comic book canon - or mainstream comic book canon at least. Singer expalined that he looked to Age of Apocalypse for inspiration on switching up traditional comic book depictions of the villains and heroes.
"[It's my] kind of my homage to the Age Of Apocalypse comic - everyone sort of switches roles. Obviously I didn't tell that full story, but people's sides are switched, alliances are changed. I think [Mystique's] right for [a standalone], whether it's Jennifer or not. She has this different view of the world: Xavier can get into Cerebro and look at the world but he'd rather just teach classes and see the beauty of mutants and humans co-existing in his mansion in Westchester. Along comes Raven with a reality check on the state of the world. It opens up a lot of avenues."