People in the marvel comic universe are very complex and also hypocrites.
Lets allow a freak like the Thing to do his stuff freelly but lets arrest and register normal looking kids like Kitty Pryde because she is Homo Superior.That makes sense.
Racial prejudice
doesn't make sense, that's the point. It's an ignorant and irrational fear and hatred of something born different. With mutants it's elevated a
lot further because of the likes of Magneto openly advocating mutant kind should take over the world with humans eventually being wiped out (and that was pretty much the
first thing he did in X-Men 1 btw).
X men clearly belong to a different universe its such a mess in the comics.Im praying the movies will not make the same mistake
In regards the respective movie continuities, certainly, they are 2 different worlds and they couldn't just fit the X-Men world in.
Now In the hugely unlikely event Marvel were to get the X-men rights back they could (and certainly would) start over.
Remember, in the comics mutants were an unknown before the X-Men. The first superhumans the world was exposed to were the Fantastic Four, who never hid behind any secret identities. This was later revised so the Invaders of WW2 were the first, but back then Namor was not recognised as being a mutant.
Now imagine if the Marvel Movieverse world's first exposure to mutants was Magneto going on the rampage (as it was in the books). Now even if the public see him being stopped by good mutants, it's not too hard to see how the public perception of this 'new' race of beings, calling themselves 'homo superior' to boot, would not be too favourable.
Bottom line is that I think the X-Men, and the whole concept of mutants, could work just fine in the Marvel Movieverse. Cannot say I think that would ever happen though.