From what's known, apparentally Edward sort of wanted too much control over the character, and a lot of Incredible Hulk was rewritten as a result. Marvel studios was not happy with this, there was some dispute and Norton walked out of the Avengers project. I'm not sure about Ruffalo, his Banner is apparentally more of the Bill Bixby mode than the 'puny' Banner of the comics (Which Bana and Norton were mostly based on).
It's been mentioned that Incredible Hulk will still be part of the Avengers 'canon', and possibly explain why Banner was able to trigger a transformation at the end of the movie without getting angry.