What if Marvel/Disney one day somehow got the rights to use Mutants and other X-Men related property? How could you possibly introduce the concept this late in the game? Surely the existence of mutants and Professor X and the X Men etc would have come up already at this point?
The following is my solution.
Imagine being dropped into an action situation of some group of fleeing mutants (198 or so) escaping some death-camp scenario. Even some familiar heroes from the MCU are in pursuit. The leadership of the escaping mutants is made up of whoever Cyclops, Wolverine, Beast, Grey etc. They fight sentinels and their government while they debate their options. Having nowhere is the world that is safe for them they only have one choice, to leave their world behind.
This opening is also your opportunity to kill off whatever X-men you don’t want to use whether to avoid repeating their use in FOX movies or for shock value etc. This is also where you kill off a couple recognizable characters from the MCU who are noticeably out of place in this strange situation. Finally Professor X will sacrifice himself so the group can escape.
It is also important their escape is facilitated by some familiar heroes (and/or villains) from the MCU, like Captain America or Doctor Strange. Again it would be best for one for two of these characters to be killed off here as well.
Cut to the MCU we all find familiar. Immediately its clear this is either another world or another timeline then in the first scene because we see characters who are alive here who we saw die moments ago. Things seem back to normal, a continuation of the setting/timeline established in the previous MCU movies.
Tony Stark or someone else from the MCU is at Xavier’s School for Gifted Youngers, giving them a new wing or a piece of educational technology like a fancy computer. Xavier is seen alive and well and he being applauded rather than hunted like before, further proving we are in a different world then the one we just saw.
The twist is this version of the school appears to literally just be an academy for gifted kids, and Xavier is just a kind man who can’t walk with nothing exceptional about him beyond his good character. Because in this world, as we all know, there are no mutants (only inhumans…)
Professor X has an Obi Wan Kenobi moment that another dimensional version of himself just cried out in terror and was silenced. But he brushes it off to give a nice speech about everyone having some gift, something special inside them
The benefactor (Tony or otherwise) has their photo-op and it then interrupted with Avengers/Superhero business.
Or more accurately “Illuminati” business. Members of the MCU version of the Illuminati meet, Tony Stark, Black Panther, Doctor Strange (possibly an Inhuman if they are more firmly established at this point). They give the exposition that they formed this secret group to come together to meet on important happenings to protect the world etc. Doctor Strange has called the meeting. He enlightens the group on alternate realities. Not just fantastical dimensions but also more familiar alternate versions of earth. Places where things turned out differently. Some differences may be small while others tremendous. Strange explains that when he meditates recently he has been in contact with different versions of himself from different timelines and one of them has asked for his help.
In this parallel dimension (call it 616) mutants were a known phenomenon predating captain america. However they have entered troubled times and their kind, once in the millions, are all but extinct. The “prime” dimension of the MCU doesn’t have mutants because of a mysterious event in its past that eradicated their kind from the world. So the Doctor Strange from 616 believes (and his other versions agree) that since the “prime” dimension doesn’t have any mutants they have the most room to take them in?
The Illuminati debate the issues of allowing sanctuary to 198 “special” or “advanced” individuals but Strange confesses they are already here. That he already assisted in their travel to their world by metaphysical/mutant power/scifi tech means. So folks just gotz to deal with it.
Lots of story potential would be opened up here (not even including doing 616 based movies in a timeline that predates the house of M style situation that sparks the cross over)
The mutants can tentatively settle at Xavier mansion with the special kids, and powerless Xavier can learn about his other self. Obviously a lot of plot can be mined from the powered mutant versions of characters meeting the unpowered local versions of themselves if they exist. “what makes a hero” type stuff. You can get some originally out of the “mutant question” because they are also now like refugees.
You can differentiate the mutants from the Inhumans because the Mutants can seed the idea that in their dimension, Inhumans and Mutants are distinctly different groups and how their 616 Inhumans have mostly immigrated to the moon (leading to a moon colony of Inhumans in the MCU who like the sound of the idea?).
You kill off Captain America in the MCU? No problem, you’ve established another dimension where you can steal yourself a new captain America.
Tension can be provided by evil forces from 616 coming to hunt the escaped mutants, from the refugee mutants struggling to settle and of course through exploration of the mutant gene. What suppressed it to stop mutants from developing in our world? Was is a mutant power? A hydra plot? Alien intervention? How could the effects be reversed?
Never gonna happen. The MCU will be over by the time there is even the legal framework for a truly unified cinematic marvel universe. But one can always dream