Yeah, now that I think about it more, that probably would be a better way to do it. That way they can keep what makes them unique, and they won't have to deal with rewriting the whole history of MCU, and try to deal with how the FF and X-Men being around would have effected what didn't or didn't happen in new universe. We saw how much of a nightmare those kind of retcons can be with things like DC's post Crisis reboot and the New 52.Would be cool if Reed Richards comes up with a way to save their universes from 'merging', but the resultant save is like a gateway connecting them where each universe pulls on another to maintain some type of equilibrium.
Which would leave them their own 'stories', but also the possibility of crossovers. I also personally really REALLY don't want to lose the '50s/60s futureworld' look in the Fantastic Four movie.