I've played it through several times.
The woodsprites in the credits are not the same as the movie. I think the game was already in development before that aspect was finalized or they never got more than a text description to work with.
The railgun turret and car from the game are only seen once in the movie, both in the opening Hell's Gate landing scene.
It's possible to play the entire campaign without noticing the RISK minigame in the teleportation tree menu. (I'm guilty of this.)
The tufts of fur at the tip of Na'vi tails are missing.
It's been a while; I'll post again if I remember anything more interesting.