It wouldn't make sense for him to work on something else when he's supposedly been working with Stark after The Avengers.
Now, since the whole reason he was brought along was because there were signs of gamma radiation from Loki's attack. It's possible to make a movie where he is working with SHIELD and something creates another gamma mutant. It wouldn't be far from what he's had to face in the comics. Although a Red Hulk storyline could be interesting.
Either way, nothing going on has really lent itself to an Eco-message. Maybe he could try to get SHIELD to use their resources to create clean stuff instead of purely military. If it doesn't fit it doesn't work though, and if you start out from, "It must have this message," it's as bad as starting a movie with action scenes in mind first. But Joss Whedon is fairly liberal, so maybe he would let it slide.
I have just seen perfectly good movies ruined by throwing in a preachy message that doesn't fit in with the story.