Right from the appearance of S.H.I.E.L.D and Nick Fury in 'Iron Man' the Marvel Cinematic Universe (MCU) has been about expanding the context of it's films to create an ever growing cohesive environment. With each new film the links have increased and the scope of the MCU has grown wider. However, this creates it's own problems as on one hand Marvel want to release sequels to popular films about established characters (as seen by 'Iron Man 3', 'Captain America 2' & 'Thor 2') but on the other it wishes to introduce new characters and concepts (as seen by 'Guardians of the Galaxy').
Of it's ongoing franchises there are issues going into Phase 3; 'Iron Man 4' would be a financial success but another Stark solo film is unnecessary, and may not be possible. 'Thor 3' is an option but more on that later. 'The Incredible Hulk 2' is unlikely as despite the success of the character in 'The Avengers' neither Ang Lee's 'Hulk' or the reboot were financial/critical successes. 'Captain America 3' has the risk of being a bit redundant follow his WW2 origin film and one modern day first sequel.
With a limited number of Phase 3 films that can be released between 'Avengers 2' and 'Avengers 3' the solution would be to release a 'Team Up' film of two established characters, namely Captain America and The Hulk.
'The Incredible Hulk' is strongly linked with Captain America's Super Soldier concept via General Ross restarting the Super Soldier Program, Banner's work, the creation of The Hulk and the eventual creation of The Abomination. Now both characters are present in the same time I would like to see them brought together in a Team-Up film.
A rough idea for a plot could be as follows: After his ambiguous ending in 'Captain America: The First Avenger', Red Skull reappears in the modern day. He wishes to mobilise the remaining HYDRA troops but is now without the Tesseract and could be facing the might of The Avengers. A way to increase his threat would be to create his own Super Soldiers using the same serum that created himself and Captain America (as well as Hulk, Abomination and The Leader). In order to have someone with knowledge of the Serum he can break The Leader out of S.H.I.E.L.D custody, as well as The Abomination as some additional muscle/guinea pig. S.H.I.E.L.D can then call in Rogers and Banner to tackle this evil alliance...
Some pros to this idea are:
It gives people a Hulk sequel but with less financial risk than a standalone film.
It pleases people who moaned that Tony Stark didn't receive help from any other Avengers in 'Iron Man 3'.
It ties up loose ends with the villains from 'Capitan America: The First Avenger' and 'The Incredible Hulk'.
It bring the 'Marvel Team-Up' comic concept into the MCU.
It ties in with the themes explored in Captain America, Hulk and Iron Man films.
A Team-Up film could help move the overall Phase 3 story arc along, leaving the new character films like Ant-Man to concentrate on their own origin stories.
A Team-Up film combines two franchises leaving a free spot for a film with a new character (e.g. Black Panther)
If it is a success it opens up the idea for other Team-Ups; 'Thor & Guardians of the Galaxy', 'Heroes for Hire', etc.
With the characters already established this film could help move the Phase 3 story arc along. For example, a lot of people assume that 'Avengers 3' will be an Infinity Gauntlet style story. This Cap/Hulk Team-Up could link to that with Thanos bringing Red Skull back (similar to Loki) and using him to perhaps gain access to an Infinity Gem. Once Red Skull, The Leader & Abomination have created the super soldiers we could have an epic fight in which Cap/Hulk destroy the super soldiers but are weakened from the fight and the villains use of the Infinity Gem to power HYDRA's weapons. With our heroes seemingly beaten Thanos could return, kill(!?) the bad guys and steal the Gem. He could perhaps briefly fight the Hulk, or maybe even casually dismiss the heroes before disappearing. This would wrap up all the loose ends for Cap/Hulk, show the power of Thanos and even give a personal grudge between two of the Avengers and Thanos before his major appearance in 'Avengers 3'.
Obviously this is pure speculation and it's hard to guess what will have happened to Cap and Hulk between now and Phase 3 (especially with 'The Winter Soldier' and 'Avengers 2' being released before then). However I think this would work well as an alternative third entry to the Captain America trilogy and I would love to see Marvel do something similar to this idea, perhaps calling it “Captain America versus the Super Soldiers!”