With the Fantasic Four reboot in the pipe line and First class sequel on the way from Fox, a few unchecked cracks are going to start to appear. Especially, since Marvel is moving into Phase 2 with their films, most likely leading up to an avenger's sequel.
An interesting question arises with a few characters :
Who do Scarlet Witch and Quicksilver fall in with, the X-men licence under Fox or the Avengers licence in Marvel Studios? if it's Avengers this leads to a quick but deep follow up question. If things go as well for the franchise and we get to a young avengers movie... how do you do Hulkling? Teddy is Half Skrull and Half Kree, Skrulls AND KREE fall into the Fox licences properties with fantastic four. So you'd literally need to change Teddy's background to make it fix without mentioning skrulls... Same thing with Runaways' Skrull.
Which leads me to another question with a smaller character the Skrull Crusader(Z'erg), he wears a piece of the cosmic cube fashioned into a ring, is an avenger in training and a Skrull at the same time....which way does he go?
I hate rights battles, but these are some of the things I end up thinking about.