As I have not read the novelization or played all the extra content of the extended Blu-Ray or perused the coffe table "behind the scenes" book, I'm sure there are details I've missed, but just watching the movie, I got the impression that the Na'vi may not be fully indigenous to Pandora.
They possess 4 limbs and just two eyes whereas all other higher vertibrates have 6 limbs and 4 eyes. Plus the nerve tendril business, the "horses" and the banshees have two while the Na'vi just have the one.
I'm sure the more attentive viewers consider this "old news", but I have not engaged in those discussions. I would think that's potential for story right there. Just why ARE the Na'vi so fundamentally different from all other (so far seen) higher life-forms on that world? Do you think Cameron will explore this?