Why I thought he should be in Iron Man 3 was because of the developing relationship with Tony Stark we saw in Avengers. I wanted to see more of that.
But there's another possibility that's somewhat more intriguing.
Bruce Banner isn't just the person who can turn into The Incredible Hulk, he's also a very good scientist. Tony Stark is a science heavy inventor. In fact, the Marvel Universe has several excellent scientists it can call on.
Imagine a movie where the problem couldn't be solved with superheros but instead needed
Tony Stark is the genius who can invent whatever it turns out is needed. Bruce Banner and Betty Ross are both top scientists. Banner knows more about gamma radiation than anyone else on earth, Ross was his colleague and, by all accounts, equal. If Banner is the top on gamma radiation then Ross must outstrip him somewhere else.
Jane Foster is one of the two foremost experts on portals and the fabric of reality and all that stuff. She has a sidekick she can bring with her. I've previously pointed out that the giant gaping plot hole in the Avengers is that they didn't call Jane Foster in. Erik Selvig is the other of the top two experts on portals but after the Avengers he probably needs some time off at least a portion of which is spent with a therapist.
So right there we've got Banner, Ross, Stark, Foster, and Darcy Lewis (Foster's sidekick.)
Four well studied people who have achieved genius either through natural inclination or hard work (or both), and one less academically advanced person to keep them grounded and remind them that common sense can still work even when dealing with holes in the fabric of reality (and carry a Taser.)
The hard part would be finding a problem big enough that they couldn't solve it by sitting around a table in a coffee house and talking for half an hour while writing on the backs of napkins. This would have to be something that goes beyond aliens invading New York, it would have to be something BIG.
And I would watch the hell out of that movie.