Changing Juggernaut to Quicksilver when their Juggernaut actor had already been training for weeks probably had something to do with Joss Whedon using the character. Just like Marvel retconning the Daddy Magneto retcon probably has something to do with Fox using the character.
Anyway, I think a potential Sony deal could help get Fantastic Four into the MCU if next year's film fails. If Fox sees that a co-production can work they might be interested in working something out themselves (and, like with Spidey, that will mean new cast, new creative talent, and Feige on board). The X-franchise doesn't really mesh with the MCU (thanks, Quicksilver!), but it's entirely possible Fox could work something out with an MCU reboot in a few years there if co-productions are proven to work. Let's look at it this way: In a few years, nearly every major current X-film actor is probably done. Jackman's probably done with Wolverine 3. McAvoy and Fassbender may be done after Apocalypse, Jennifer Lawrence is very likely to be done with Apocalypse (Fox was, frankly, lucky to sign her just before she exploded in popularity), and most of the original cast is aging out of viability in a hurry. The "First Class Trilogy" will be concluded and Jackman could get his farewell film with Wolverine 3. Why not let the Foxverse conclude there and start up with new stories in the MCU? Heck, there are so many alternate futures and parallel realities in the X-Men comics that the current X-Verse could still be "canon", just in an Age of Apocalypse sort of way. They're going to have to recast and do stories in a modern setting in a few years anyway. Why not work with Feige and crew to tell those stories? They could even pull in "All-New X-Men" and bring the new Cyclops and crew from Apocalypse into the modern MCU (again, alternate reality could easily explain the differences between worlds).
There. X-Men fans could have their cake and eat it too. All of those Foxverse films can exist in their own canonical alternate universe/timeline continuity while the new ones with the new cast (that's almost certain to happen in a few short years anyway) move to the MCU.