The story needed Sully to be the main character; it couldn't have focussed on a Na'vi. Sully had to be "enlightened" - he had to grow and change throughout the movie. It is a bildungsroman: the character had to go through the process of maturation. Sully left behind the bad human beliefs and arrived at the good Na'vi beliefs.
If the main character were a Na'vi, then he/she would already have the correct set of beliefs (non-capitalist, environmentalist) and there wouldn't be a process of maturation. And it is not as if the Na'vi character could have not cared about the environment (been a "rogue" Na'vi who learns the true Na'vi ways) since a Na'vi like that doesn't exist in the movie - they all care deeply for the environment and are connected to it.
Therefore Cameron had to choose a human as the protagonist to show the error of our way of thinking, and who will arrive at the correct set of beliefs. That seemed to be the purpose of this movie.
