The issue isn't Deadpool per se, it's sharing the extended cast of characters - Marvel probably doesn't want Colossus running around in both franchises, and essentially cutting Deadpool off from every character that hasn't appeared with him in a movie so far is a good way to kill the franchise. Regardless, I'd wager there's a similar fight along these lines going on at Disney - namely, when it should integrate the mutant universe into everything else. My guess is the plan is not to do any such thing for at least the next three years, since the Fantastic Four's a better fit and helps fill the schedule for a few years before adding mutants.Deadpool is barely in continuity anyway. They can do what they want with the rest of the X-men properties and leave Deadpool as his own weird little siloed off R-rated comedy thing where its all played for laughs and he just pokes fun at all the other heroes. When Galactus or whoever shows up in the next Avengers movie or the X-men tackle a rebooted Apocalypse, nobody is really gonna be asking "where is Deadpool? How does he fit into this?"