The only real plotline that could redeem the whole thing as a series would be to paint things from a "proper" perspective. The results of the first movie leading to a whole lot of people throughout human space going without energy, billions suffering for the sake of roughly 4,000 beings that were in the area, and the point being made that from a certain perspective perhaps the hero of the first movie was correct, but he did not pursue the greater good and basically caused widescale suffering for a few "one with nature" soundbites and a piece of blue tail.
Show things from a differant perspective with space marines taking back the planet from a handfull of vicious natives, and an inherantly hostile enviroment.
Probably end it up with the guy from the first movie being frog marched to stand trial.
Done correctly the humans should seem like the righteous ones the same way the Na'Vi were in the first one.
Then if it's a triology you do the third movie based around finding some compromise since basically nobody can claim to be right or wrong in this situaiton. Address issues like genocide vs. morality by the numbers. Does survival make it right to victimize another species? Can a species withholding a mineral they can't even use for "spiritual reasons" claim to be right knowing it costs the lives of billions?
Oh sure it should have some happy, feel good compromise (I am nothing but a romantic in the end) when the triology is completed. However I am hoping it will not be another glorified "Sully Smurfdancer, does Ferngully!... featuring a surprise guest apperance by CAPTAIN PLANET!)
