Bioluminescence is awesome. I also really liked the scientifically valid take on the Gaia hypothesis; such unconventional concepts of life are unfortunately rare in sci-fi. (Of course the other extreme was also present, with the impossibly humanoid Na'vi, but that was pretty much necessary.)
And finally we have a movie visually surpassing 2005's King Kong. For awhile it seemed like CGI had declined a bit, but I guess the producers just weren't trying as hard.
The story was nothing great, but as you say, the telling was what made it good. It was easy to sympathize with the protagonist's dilemma, as the two sides closed in on the big confrontation and he was stuck in the middle. The characters were likable (even the villains, in their own ways). Some people are predicting that the movie will be quickly forgotten as CGI continues to improve, but I doubt that — it makes a much bigger impression than most cutting-edge spectacles. Remember what a big deal Transformers was back in 2007? And that one had a pretty good script, even.