Marvel have been put in a tricky position. In the years before they had the resources to put together a Cinematic Universe themselves, they sold the rights to a bunch of their characters to the highest bidder: as such, Sony still have control over Spider-Man and all related concepts, and Fox have retained the rights to both the X-Men and Fantastic Four. Apparently a deal's in the works about the former, but it's the latter that really causes problems. Quicksilver and Scarlet Witch are mutants, but they've been Avengers as well as X-Men. As such, they've appeared in Days Of Future Past and will also be part of Age Of Ultron, albeit played by different actors. In the MCU the source of their powers will, reportedly, be that they are "miracles", because they legally can't use that other "m" word. The solution to that problem may lie in the aforementioned Terrigan Bomb. Word on the street is that, in the comics and on screen, there's going to be a sea change where the vast population of misunderstood mutants will be swapped out for humans similarly transformed as the Inhumans, making (essentially) this new franchise the MCU's equivalent of the X-Men. With less Hugh Jackman, more's the pity.
Tom Baker is the Comics Editor at WhatCulture! He's heard all the Doctor Who jokes, but not many about Randall and Hopkirk. He also blogs at http://communibearsilostate.wordpress.com/