Marvel's licenses are specific by brand, and it doesn't preclude characters from appearing in other games. While Activision holds rights over all X-Men games (at the moment), Capcom could still make a MVC3 and include X-Men characters. They couldn't make a "X-Men Vs. Street Fighter 2" though for example, since Activision licensed the brand exclusively. Make sense?
Going forward, I also don't think you'll see Marvel doing or renewing exclusive licenses either (like Activision with X-Men/Wolverine/Spider-man/Ultimate, Sega with Iron Man/Hulk/Thor, TT with FF/Ghost Rider, THQ with SHSquad, etc), but rather they'll do licenses for specific projects. I also think you'll see Disney doing a lot of Marvel games themselves.