From what I've seen, Insomniac wants to remain as a game developer and not become a game publisher. That's the reason they went to Microsoft with Sunset Overdrive and EA with Overstrike (Fuse). If Marvel wants high profile releases like Spider-Man then they're definitely going to enlist the help of an experienced publisher to put it all together. A top level IP isn't something you self-publish and throw up on digital like an indie game.
So, yeah, I think you can count on future Marvel games being signed to one of the major publishing houses. Unless Disney wants to get back into the video game business, they'll need a publisher.
They just need to make it clear that they want high quality work that they can build upon. Shoddy cash grabs shouldn't be acceptable when you're talking about billion dollar IP. They've got to do their research and not simply trust the promises of an EA or Activision. It looks like they did just that this time around, as they specifically mentioned Insomniac.
I really, really like the approach of letting studios pitch ideas based on their choices. That puts the ideal of a quality game above all else. One of the worst things about movie tie-in titles in the past is that it was clear the studios couldn't really think of anything good or unique, they were just meeting their obligation.
Now, if I were running a studio, I'd pitch a story built around some of the more out-there adventures of the X-Men. Fighting the Brood in space, maybe, or jumping through dimensions with Magik. Then again, the X-Men license is probably a complete mess, so who knows if that's even possible.