I agree with NP tbh, as much as it'd be awesome to see a film with them in, I would rather it was separate from the MCU. There's no way they could do an entire universe crossover with the existing stuff and have it make sense even if the studios allowed it. If they were to start having mutants appearing now as a late development in the MCU the only way I can see it remotely working is with Wolverine being the one and only known, one and done as a solo film (which would have to be Phase 4 at the earliest at this rate, by which time I would guess the buzz will have begun to wear off for superhero films). A sudden mutant crisis similar to existing X-men films would simply be way too big, it would take over the MCU with all the mass emergence of villains etc.
There'd have to be a helluva lot of origin changes, as if he was still from the 1800's there'd be a burning question of why was Nick Fury/SHIELD not aware of him earlier etc.