Jake needed to be wasting away and getting sicker and weaker as he neglects his "real life" and chooses to live more in his avatar. This was hinted at, but it should have been dramatic so that by the time his lover Neytiri finds his real body in the trailer (or whatever it was), she sees just a shriveled weak wasted worm of a man, and nothing like the strong warrior she fell in love with. And then, in that context, she looks upon him and says, "I see you!" and she embraces him with love because she has come to love the spirit of the man, and not just his warrior prowess. And then have him near death at the end, but the tree does its magic and then you have a real happy ending, both a tragedy (his real body dies from neglect) and hope (rebirth at the tree). This would give the film and the love story much more needed punch.
Otherwise, as it stands, I did not believe the love story. Neytiri seems to just go for the strongest warrior, and that is very superficial on her part. As soon as Jake falls on hard times (suspected as a betrayer) she dumps him. And then as soon as he swoops in on the biggest bird, she loves him again. She is like a girl who goes for whoever is driving the snazziest car. That is just superficial, and I wanted to see her go beyond that, and love Jake even as a worm (see above). That would have been growth in her character; sad it never happened.
Other gripe is that Cameron likes his women to be Rambo. Ok, you have one female rambo per movie (e.g. Sarah Connor), but in Avatar *every* woman is rambo: Neytiri, Rodrigez, and Ripley. The film needed someone to play a girl (not a Xena). So I was hoping Neytiri would become somewhat more feminine (in the traditional sense). Even the love scene was cut short. The actress voicing Neytiri seemed to be all venon, and 99% of her lines are spat out. So this hurt the love story aspect, since she was a spitting cat and never became a cuddly cat. And for most humans, it's all about the love story, cf. Titanic, which remains Cameron's greatest triumph, and my favorite.
It's all about the characters, and the character I sympathized the most with was the military dude Quaritch: a fatherly figure trying to protect his people and do his job. You can tell he has a simple mind and does not grasp the treehugger persoective, but you can forgive him that since he is not a man of great enlightenment. You can't fault him for lacking a higher level of consciousness to tune in with the trees. He's meat and potatoes, and it's kind of sad to see him go.
Meanwhile the girl Neytiri seemed superficial as noted above, so I didn't really like her, and she is not the kind of girl/character I would ever fall in love with, and the guy Jake was kind of equivocal since he seemed to be playing both sides, and you get the feeling that if the Marines had beat the Na'vi, then he would have quickly assimilated back into human society. He is duplicitous, and when he gets caught on tape smashing the video cameras, you know he wished he could have remained sneaky, and he would have prefered to have not been outed. So he was very comfortable playing both sides, (which makes him a despicable character) and he was embarrassed to be outed. I would have prefered him to take a stand, rather than been caught on tape to his chagrin. I would have liked him to be wasting away (see above) and then get into a shoving match with Quaritch, which would have shown his courage to take a stand, but it would simultaneously been pathetic since he was a wheel bound skeleton, and then later in the final man to man fight have him enter into a shoving match again with Quaritch, but this time in his avatar body, where the tables are turned.
So anyway, the Jake character was kind of spineless, and Quaritch's summary of him is true: he found "local tail" and went with it. In a sense Jake is as superficial as Neytiri: they both side with whoever is winning, with whoever is driving the biggest car, and whoever is paying out the most.