UPDATE: After years of no one confirming anything, Mark Ruffalo has confirmed that Disney and Marvel do not have some of the rights for Hulk because Universal Studios has them. Read that post here.
A few weeks back, Disney announced they had acquired the distribution rights to all but one of Marvel Studios' Phase 1 movies from Paramount. Included in the deal are the distribution rights to Iron Man 1 and 2, Thor and Captain America: The First Avenger. Not included are the distribution rights to The Incredible Hulk, which are owned by Universal Pictures.
Fans are curious as to why Disney could not acquire the distribution rights to The Incredible Hulk and part of the reason, according to an Intellectual Property lawyer who follows this stuff closely but doesn't work with the paperwork directly, is due to the unique licensing agreement that was in place with Marvel Entertainment and Universal prior to the Disney buyout of Marvel.
It is widely known (via a quick Google search), Universal has had a park licensing agreement in place for Marvel characters in perpetuity for certain characters like Spider-Man, Dr. Doom, Hulk and Storm at their Orlando theme park. These are a few of the heroes Universal has the theme park rights for because each has its own attraction at the park, currently. Universal also can use more heroes who do not have a main attraction at the Orlando park but the deal clearly states specific characters for specific uses only. As long as Universal continues to use the heroes they are allowed to use, and as exactly detailed in the agreement, they are good to go.... forever. Or until Disney gets tired of it and just buys all the rights back from Universal Studios Orlando but that would be very costly.
This leads to the issue of The Incredible Hulk film. After Universal's 2003 Hulk movie, they decided to make a deal with Marvel to give them the movie rights back but Universal wanted to maintain the distribution rights for the green rage monster. This is where things get murky according to the IP lawyer. Disney can make any Hulk movie they want since Marvel has the movie rights but Universal will continue to distribute all Hulk films and the IP lawyer seems to think that Disney does not want to "share the profits" for any of their owned properties. Period.
However, The Daily SuperHero has heard rumors of a script development for a sequel to The Incredible Hulk. In other words, Marvel is still moving forward regardless of the issues Disney and Universal may have from past contract agreements. The renewed fandom the Hulk received from The Avengers has given Marvel Studios enough confidence to pursue another Hulk solo film and don't forget actor Mark Ruffalo is signed on to a multi-picture deal to reprise his role in the future.
Right now, Marvel Studios president Kevin Feige has confirmed the Hulk will not appear again in Phase 2 until the Avengers: Age of Ultron but Phase 3 and beyond will see more Hulk no matter if Universal is distributing the sequel or not.