I hope the MCU X-Men exist in their own universe and only interact with the Avengers in a big crossover at the end of Phase 6 or something like that. Otherwise, it wouldn't make sense. Thousands of mutants appearing out of nowhere without ever having been mentioned would be absurd.
No one BUT the persickety long time fans (and... That does include a lot of Hyesters, sorry but that's my feelings on this...) will honestly care in the least, especially in the general audience. We can talk all we want about "suspension of disbelief" being punctured or how they can't just spring this concept without some convoluted back story or whatever... Most people just won't care. Most people just DON'T care.
Probably the biggest issue fans have is the assumption that the ENTIRETY of the Marvel Comics X-Men mythology is coming along for the ride once the Mutants hit the MCU, so there's this expectation that the amount of mutants in the MCU will mirror how it's been portrayed in the comics for decades. Given the track record of the MCU I don't understand why they have this assumption given that has not been the case with any of the other adaptations. Think of the decades of lore and other characters that have been in Iron Man, Thor, Capt. America, and the Avengers, the characters with trilogies or more in the MCU... Those films after 11 years barely scratched the surface of the comic book content. Expecting a one for one parallel in the MCU X-Men is setting your sights so high you are bound to be disappointed.
It's like with Spidey in the MCU. Some Spidey fans were all incensed about not having Venom available. "Without Venom in the MCU, how can we ever get Flash Thompson as Agent Venom?!!"
Well... You were never promised Agent Venom. Expecting that the any of this is going to run in the same fashion as monthly comic books when what we have is two hour chapters made about every two years at best (some taking longer, some of the films occasionally being longer) is pie in the sky. So they are never going to be exact replicas of the comics for a variety of reasons and the last 11 years of the MCU should have educated us as fans into realizing this.
And honestly, just like every other concept that popped up in the MCU that had zero precedent in a previous film, the real reason they never mentioned Mutants, aside from the obvious real world rights issue, was because... They never mentioned them. Point blank. They weren't telling us that story so... There was no need to reference any aspect of it. There's no mention of a spider powered vigilante operating out of New York and then suddenly in Civil War he's there. We hard core fans can say that Spidey's introduction is clunky in CW but... The rest of the audience just didn't care. "Oh... Spider-Man is in these films now? Cool!"
It's funny that fan opinions on these things sometimes mirrors the world view of Hollywood producers from the pre-CBM boom. "Well... We need to do some kind of radical change for this to go over with general audience, because I myself can't wrap my head around this concept."
The general audience doesn't go to these films, with good or bad outcomes for the products themselves, for some kind of air tight logic about the nature of these fantasy worlds. They don't take them THAT seriously. So when the X-Men show up only an easily dismissable amount of the people buying tickets will have qualms about them being introduced without having been continuously referenced the previous 11 years.
This need to wall off the Mutants into a separate continuity is so odd to hear when for more than a decade that's what's been the status quo within the MCU and literally daily online forums were filled with fans lamenting this... Only for now many of the same fans are asking for the X-Men to be walled off into their own separate continuity.
It doesn't make any sense to me.