This was a very very good call. I remember your original post on this and your analysis seems to be on the right track.
In the movie, humans couldn't breath on Pandora due to high green house gas levels in the atmosphere, particularly Carbon Dioxide. What would cause the increased Carbon Dioxide levels? Destruction of plants that act as carbon sinks.
So logically, years after RDA is finished, it would make sense for them to have a resurgent plant life returning to its' place as a carbon sink. That would theoretically halt global warming and make it possible for humans to breath again.
That's how I except the story to go.
Along with the plant
@sedati identified, there's another species too. Vein Pods, that suck the methane out of the air and store it inside their bodies, thus acting as a major methane sink (another green house gas). If RDA had carelessly destroyed thousands of acres of forests that had groves of these vein pods, that could seriously up methane levels.
https://mobile.twitter.com/visitpandora/status/839596716705923073/video/1
I'm starting to think that the next movie will start with Pandora slowly dying. How do the Navi work through this and convince the rest of humanity that they need to fix the mess they made. I'm not exactly sure how you make that into a 5 movie saga though. They're going to need
a very good story. I'm a tad worried that James Cameron now has all the time in the world and all the money he could ever want and that him without those constraints could be problematic. Star Wars Prequals are a warning sign. He needs to tread carefully.
By the end, I think everyone will agree there's no need for a sixth film...