When and if Disney pulls the trigger and completes their buyout of 21st Century Fox, superhero fans of course have their priorities straight: get the X-Men and Fantastic Four integrated into the Marvel Cinematic Universe as quickly as possible.
There are, of course, a few possibilities to consider.
If Disney wanted to continue the current timeline, they could do so -- and simply pretend that mutants have been there all along. This would allow the X-characters to be folded into the MCU while still releasing the currently-in-production X-Men: Dark Phoenix, as well as projects like Deadpool 2, The New Mutants, and the like.
The downside to this is that it would likely conflict with some of the established history of the MCU, and confuse fans somewhat, since the current X-franchise dates back to X-Men: First Class and has been woven through decades of real-world history, right up to the modern day.
Retaining the current continuity would also raise questions about what version of the X-timeline "counts," and about whether Logan is the inevitable future of it all.
A way around that would be to go in the Spider-Man: Homecoming direction, essentially rebooting the universe and building it around the existing structure of the MCU.
The downside there, of course, is the opposite of what was just discussed: you can introduce mutants, but you can't do so and still retain the history that has been established before now.
A potential compromise might be for the X-Men movies to become non-canon, allowing for a reboot in the near future, while the Deadpool franchise and related upcoming films like New Mutants and X-Force could be integrated into the MCU. This might work more easily because they are set in the present day (or thereabouts). It would also allow the First Class X-Men movies to go out on their own terms, as they began, presumably with Dark Phoenix.
Of course, "The Dark Phoenix Saga" in the comics was a massive cosmic event, and a character as powerful as Dark Phoenix is not averse to things like time travel, reality distortion, or massive psychic changes to the characters of the world. Could they simply use some kind of massive cosmic change in the upcoming movie to forcibly integrate the two worlds and allow for a shared future? It seems the least likely possibility -- but still believable enough.