Disney has a strange contract when it comes to the Marvel stuff though. I was in Disney World earlier in the month and talking to one of the employees, it turns out they're not allowed to even have even one piece of Marvel stuff inside their parks. Universal holds the rights for that stuff in amusement parks for whatever reason. I wonder if something similar might be in place on the movies, make all the money you want, but keep your logo off of it.
But whatever that rule is, you're right, I don't think they'd do much logo-wise with the new movies. But the one thing that will be really strange, and I think it was mentioned here, will be the opening of the movie without the 20th Century Fox stuff. That music flowed into the opening theme so perfectly.