Marvel's got a lot of bitterness about not owning the film rights to Fantastic Four and X-Men (in case you couldn't tell), and their adversarial relationship with Fox doesn't end at merchandise and cancelling series (although this one does make a bit more sense). Since Fox owns those two comic book universes, they also own any new characters that are introduced through those books, so Marvel's just not gonna do that anymore. Any new characters must first be introduced through another title - Hulk, Iron Man, etc. - and not introduced as being a mutant.
Marvel's actually taking this a step further in January 2015 - when they launch an event titled "No More Mutants." See, Fox owns more than JUST the X-Men franchise - they own usage of the word "mutant" too. That's why Quicksilver and Scarlet Witch were referred to as "miracles" in the post-credits scene for Winter Soldier - Marvel legally cannot have the word "mutant" in any of their films. So (as rumor has it) Marvel decided that, instead of working around these restrictions and using different sets of terminology for their movie and comic book universes, to get rid of the term "mutants" and start calling them "miracles" / "gifted" / "inhumans" or something else entirely. And who are the poster children for the event? Why, it's the only two characters that both Fox and Marvel claim rights to: Quicksilver and Scarlet Witch!
Marvel's not the only one with spite in their hearts - Fox reciprocates in kind as often as possible, as seen with the whole dueling Quicksilvers thing playing out in cinemas. Originally, the script to Days of Future Past called for Juggernaut to be the mutant (OR "NON-MUTANT DUDE WHO HAS A MAGIC CRYSTAL," PEOPLE ABOUT TO CORRECT ME) who helps break Magneto out of the Pentagon - but at the last second (which is pretty literal here - this was the last thing filmed) they replaced it with Quicksilver...right after Joss Whedon and Marvel announced Quicksilver would be getting added to The Avengers. Here'a look at the original concept art for Juggernaut by Anthony Jones:
Quicksilver and Scarlet Witch are the weirdest rights characters - their comic book history allows them to be used by both Fox and Marvel (although Marvel apparently cannot mention their parentage, nor - again - call them 'mutants'). When Fox decided to shove Quicksilver into X-Men: DOFP, it seemed like a hasty spite move, guaranteed to be shitty as a result of their rush to be first (especially after the character was introduced in a Hardee's commercial). Weirdly, the Quicksilver sequence ended up being probably the best part of the entire movie, and now the ball's in Joss Whedon's court to do something weird and different.
Maybe have him trip over something while running and have the most gruesome death scene in film history? Really, we wouldn't put it past Whedon.