5 Ways To Improve The X-Men Timeline
3. Kang The Conqueror
If Fox still holds the rights to Fantastic Four then they have Kang, and while this could open up a whole other can of worms later down the road, he is a time-traveling villain with ties to Apocalypse. They could have him traveling all over time, going far back enough to effect things multiple times, creating many branches off of the same timeline, like we have now.
With the Shi'ar potentially on the horizon due to talks of the X-Men films going cosmic in the tentatively titled X-Men: Supernova, they could exploit Kang's connection to Apocalypse and reveal that the golden tip upon Apocalypse's pyramid that allowed him to continuously transfer his consciousness to new bodies was possibly Shi'ar tech. So, that basically connects him to old films and new ones and paves his own way as a force to be reckoned with, a villain that can hop around time and thusly change the very timeline he's entered.
Something else of interest to Fox in this matter is that it would provide a tangible connection between the X-Men and the Fantastic Four. They could even have the Shi'ar be the ones who transform the group into being so "fantastic" after their fateful mission into space, though that would certainly disappoint some long-time fans of the FF. But from that eventually arises Kang the Conqueror and he may even use Doctor Doom's own time-travel tech to do his damage to the timeline.
Now, the real question is if the connection between X-Men and the Fantastic Four is even desirable or not but that doesn't stop it from being on Fox's radar. It may still come to pass and if it does, they might want to consider this possibility before they waste the opportunity.