Fox only has the Film rights to X-Men... that does not include Television Shows. The television rights for X-Men, I believe, either reside with Marvel themselves or if not with the parent company. That is the reason why Wolverine and several X-Men appeared on Super Hero Squad and Avengers: Earth's Mightiest Heroes. If Fox had held the Television rights to X-Men, Wolverine would not have appeared as such in those shows, nor would the cameos of the X-Men occurred.
The only thing preventing Marvel from a new X-Men animated series is likely airtime, financing, and storyline.
I myself wish they would create a new X-Men Animated series and have in my spare time written three series bibles for potential X-Men shows. Granted the likelihood of Marvel accepting a bible from a writer that has not worked in television or comics before is slim to nil. Granted that won't stop me from adding them to my Devart account, or uploading them here once they are compiled, as I plan things with a typewriter.