One thing I found frustrating was the reveal of the sentient planet, and how apparently every creature on Pandora has a plug in their heads to tap into the vast hive mind. That's just such a fascinating concept, and I wish that had been explored a little more. I mean, was life on Pandora engineered somehow? Could such a thing evolve through simple natural selection?
And of course that leads to a whole host of story problems. If you're able to plug yourself into any other creature on the planet, see what they see, feel what they feel - indeed, if you're able to access some planet-wide organic memory bank that stores the consciousness of every individual, living or dead - you're not going to be a hunter-gatherer society. You're going to go vegan in about three seconds flat, just so you're not haunted by the memories of being devoured by yourself. Being a hunter on such a world is vaguely disturbing, to be honest. No matter how respectful or merciful you are about it, you're one extension of a collective consciousness killing another extension, with the implication that the consciousness as a whole is okay with this arrangement.
And that further makes the movie's condemnation of the human race a little unfair. I mean, it's not our fault we evolved on an indifferent planet! It's not our fault we don't have organic USB ports in our heads! We didn't kill our Mother; we never had one in the first place! All the Wolf-Dancing stuff about living in harmony with nature is pretty convenient if you live on a planet where nature is capable of telling you what to do.
...I just put more thought into this than James Cameron did, didn't I?