Having Franklin be "god" may be a bit overpowered, but having him have zero powers and playing the older sidekick to Val's "kewl" is getting quite old. The kid's been around since 1968, he deserves better than to be Val's Ron Stoppable. Surely there is a safe middle-ground of Franklin having potent psychic powers, but not being a cosmic being yet.
Considering he is one of few mutants left on the planet to retain his powers, you would think some of the problems the X-Men still face would intertwine a bit with the Four. After the 80's, I doubt they did. While the X-Franchise isn't exactly healthy, either, UNCANNY X-MEN still sells aces above FF.
Ideally, the Fantastic Four should be involved with most of the universe they are in, whether aiding in "ANNIHILATION 4" at some point, or interacting with mutant elements that the X-Men are more used to handling, and Dark Reign and everything in between. Just keeping them on the sidelines for whatever stories a creative team has is limiting. The Four were often front-and-center during their heyday during the Lee & Kirby era, and even some of the eras after that. While I doubt that will happen again with Marvel behind the Avengers now, they surely don't have to be a niche franchise yet.