To be honest, as much fun as it might be to see huge crossovers, I prefer to have the X-Men universe stand on its own. It's difficult for me, personally, to reconcile the treatment of mutants by humans when there are countless other 'regular' humans out there with superpowers, too. I know it's been touched on in this thread and in others, and some people don't have a problem with it, but I just find it odd. So yeah, while I'd like to see Marvel get full control of the X-Men property again, I kind of like that it's under another studio's control because I prefer the X-Men to be in their own universe.
I don't think the instances of bigotry and prejudice that exist in the X-Men movieverse are incompatible with the filmic Marvel U as we've seen it thus far, especially if you use First Class to effectively reboot the X-Men film franchise because you'd then be able to integrate the bigotry and prejudice issues into what we know happens in the future of the filmic Marvel U without any major issues or problems.