According to Producer/Writer Simon Kinberg, the originally planned for crossover of the FOX superhero properties is no longer happening in this current batch of releases (Days of Future Past and the upcoming Fantastic Four reboot).
In an interview he did with the folks at Empire Magazine, Kinberg suggests that the Fantastic Four as they currently exist don’t really justify their moniker when stacked against the breadth and power exhibited in the X-MEN universe. Simply dropping them into a world where mutants exist would be a disservice to the characters. Read more of the interview excerpt from Empire.
As a fan, I’d suggest Kinberg doesn’t really have a good grasp on the Fantastic Four if he thinks they can’t hold their own against the mutants.