I don't think we'll be seeing Mickey Mouse in Marvel Ultimate Alliance 2 (certainly anytime soon), but with Disney Games making very honorable efforts, like Split Second (pictured below) and Spectrobes, I don't think Activision will be making Marvel Ultimate Alliance 3. Obviously, there are many implications in the area of where Marvel licenses will lie in the future, but until those licenses come up, Disney won't be spending the cash just to get them in their stead.
Instead, I think we can expect to see Disney pouring more and more money into their Interactive Studios division. We'll be seeing a lot more intellectual properties coming out of Disney, along with renewed efforts in the Disney branded games they put out. I think that they're going to muscle up in the video games division so that as the Marvel properties become theirs again, they'll develop in house.
It's a pretty clear cut deal across the board for Disney actually. They stand to do nothing but gain from the IP Marvel owns. Imagine the Spider-Man ride Disney could come up with. More importantly I think we'll be seeing more of everything once Disney understands to keep their name off of Marvel's work as much as possible. They should be very careful, because some of the younger male adolescents out there could become alienated by the very nature of Disney. I know growing into a teenager means that Marvel becomes cooler than Disney, and how can it do that if Marvel IS Disney?