What I really think Marvel and the other studios need to do is work out some kind of shared custody of the Universe kinda thing - I mean the above poster saying that "well the X-Men's civil rights issue would be undercut by the FF" - which is pointless really since in the main Marvel Universe -the FF are right there alongside the Mutants and such. But it's the Mutants that get the flak. Could actually be an interesting story - the Fantastic Four or Avengers or some other super heroes do the same thing the X-Men do, but the X-Men have bottles thrown at them and told "Muties go home!" while the FF are given awards and people ask for their autographs. Sort of a "well that's not fair, they got powers too."
I think it could work. I still see no reason why a rebooted FF couldn't play nicely within the First Class rebooted X-Men really. Or why they couldn't name drop from the Marvel Films and Sony. ASM almost did cross over with MF and y'know even in the comics each character and team can be totally indepedent from each other. X-Men stories usually focus on just the X-Men, same with FF or Avengers. Heck, it feels like that failed inititive from the late 90s pre-Heroes Reborn when Marvel was segregated. Spider-Man was it's own little pocket. Avengers was in its own little pocket. X-Men were in their own little pocket. Marvel Edge was the "supernatural and more 'edgy' stuff like Ghost Rider, Nightstalkers, Punisher, Morbius. It wasn't until the Onslaught event that they changed the editorial mandate and let crossovers happen again.
Their thing was a few characters here and there could cross over as long as it didn't interfere with what was going on in other stories. Like if say, Human Torch wasn't really being used, as the current FF stories were all about Reed and Sue, then Torch could pop up in Spider-Man but that was about it. Each editor had their own "domain" and that was that.
It seems like that is what is happening with the movies and TV shows - you've got the X-Men with one "Editor" , the FF with one "Editor" you got Spider-Man with one "Editor" and the Avengers and the general "Marvel Universe" under another.
Although since Disney does have deep pockets - hell they own Star Wars AND Marvel sooner or later Disney is going to get it into their lawyer's heads that the only studio that "Deserves" to have the valuable IP that is the Marvel Universe is Disney/Marvel Films and Sony and Fox will eventually lose what they had - which would be a good/bad thing since that'd probably mean we'd get 'reboots' again...