Here is how I think Avatar should have gone. They wouldn't actually have had to change a whole lot.
The girl - whom I shall have to call Pocahontas because I cannot be bothered to remember her real name - should have been either a protagonist, or at least had a larger role. Yeah, granted seh was in most of the movie, but mostly in the capacity of teaching Jake Sully, aka John Smith, the ways of her people.
Okay, so my revisions mostly involve making Jake Sully not save the day.
What he does in the movie: Warn them what is coming, tame a huge flying creature that has not been tamed in generations, use this creature to inspire the People to inspire the rest of the people to come and help, ask Eywa for help (which she gives, which is what saves the day).
What should have happened: JS warns them what is coming. Tree is still destroyed as happens in the movie. Pocahontas decides after she realizes the extent to which JS betrayed her and then watches her father die, that she must take it upon herself to rally her people. So she goes and tames the giant bird thing - she has more experience with that sort of thing anyway. Maybe they could even have worked in something where she thinks of doing that because she has been hanging out with JS who has weird/unorthodox ideas if htey really wanted JS to help more. Then, she rallies all of the clans on the planets (which, by the way, didn't exist before that time as far as I remember. Were they previously mentioned?) . JS can still be the one to ask Eywa for help, because the People have always been taught that Eywa does not take sides, so it doesn't make sense for them to do it. And JS is the only one that knows the extent to which they are all doomed. OR Eywa could have taken it upon herself when that huge tree got destroyed, but perhaps that would have been too LotR.
That would have made this a significantly less white-man's-burden/guilt movie.