oh man OH MAN
I can see it now.
Phase 5 or some shit, after Marvel somehow wrestles back the X-Men rights. First film opens with "no more mutants." Rest of the film is a flashback. We see the X-Men throughout various events in the MCU. They were there in Avengers 1. Hell, they were there in Avengers 2 and 3. Played a huge role in the Infinity Gauntlet. Rest of the film is new events, heavily features the typical "world hates mutants" trope. Lots of infighting. Various plot whosawhats. One way or another, builds up to Scarlet Witch erasing mutants.
But the MCU twist is that she does it Sentry-style. Not only are they all depowered, but the world forgets they ever existed. Everyone remembers a world where the heroes in the Avengers film were the first real appearance of super-powered heroes, despite a "true" history where there were decades upon decades of mutants.
Scarlet Witch and Quicksilver are the only ones that survive the cull, and they remain in the world's memories as a part of the Avengers. Maybe she reverses "no more mutants" at the end of the movie, or maybe X-Men 2 is about the magic wearing off naturally, and the world coming to grips with these mutants in their midst, memories coming back and powers re-emerging. Which, with the heavy Avengers focus the MCU has had, dovetails brilliantly into Civil War.
aw now I made myself sad