Wrote this in the FF forum:
Originally Posted by Shikamaru
The X-Men have always had trouble fitting into the Marvel universe as a whole. It takes a certain level of suspense of disbelief to accept the fact that, in a world inhabited by so many superheroes that were not born with powers, people born with powers are discriminated towards and not accepted by society. Sure that there are ways to make it work - i.e. the Stan Lee approach or the "we fear them because they will take over the human race" approach - but if in the X-Men comics themselves, it seems that mutants are feared for the most part simply because they have powers. The same argument could be applied to the mutates. On top of that, the X-Men universe at large is almost about the same size as the rest of the Marvel universe and whenever there is a big Marvel Universe event, the X-Men seem to be excluded for the most part other than Wolverine and a few other mutants. Same thing applies to the rest of Marvel whenever there is a big global X-Men event.
Like I said, there are ways to make the X-Men believably coexist with the rest of Marvel but I don't see Fox being able to pull it off especially with a property as lighthearted as the Fantastic Four.