I actually prefer having the X-Men movies in their own, separate universe. I wish the comics were the same way. I also don't mind Spider-Man being under Sony's control, since I prefer Spidey on his own. If it were up to me, I'd split the big Marvel properties up like so:
Marvel/Disney: Avengers, Fantastic Four, SHIELD, etc.
Sony: Spider-Man and Daredevil (so that they can share the Kingpin)