For me, the biggest problem was disappointment and frustration. To be totally fair, when I went to see it in the theatre, my primary interest was in seeing the pretty 3D visuals (yes, they were very impressive) and I didn’t have high expectations for the story. However, it delivered a story even poorer than I expected. My frustration was that it (as far as I could tell), it shouldn’t have been to difficult to improve the story.
I’ve found most of Cameron’s stuff in the past to be at least compelling enough that I wasn’t overly bothered by plot holes until I thought about it later: while watching Avatar, despite the pretty visuals, I found myself thinking “holy crap, this is stupid.”. I could have accepted the whole “Pocahontas in Space” storyline if there had been an effort to deliver more about the conflict beyond “duh, humans and corporations are greedy and bad, and are going to destroy the noble savages to get this McGuffin element”. A line or two of dialogue could have added logic to clarify and maybe decrease the mess. Make this bullshit element something essential for the survival of the remaining humans in space (I dunno, maybe it’s key for generating artificial gravity or something). Doing that raises the stakes and while the humans are still short sighted idiots for the stuff they did in the past, and things are still being done in a nasty, greedy way (someone’s still likely to be making money off this stuff), it also gives a compelling motivation for the human side of the conflict. They’re still assholes doing things in the wrong way, but they’re desperate assholes.
Just my opinion, YMMV.