magic - although the movie makes anything even slightly mystical have some scientific sounding answer (although still quite fantastic), the game incorporates elements (not seen or even hinted in the movie) that are impossible to explain away as such (many of the "skills").
upgrade system - hidden behind the conquest minigame.
no children - although this makes sense for the RDA, the Na'vi villages, especially the hometree, are oddly devoid of children.
Na'vi specific: bows, crossbows, riding, melee weapons, summoning
RDA specific: all firearms (except machineguns), driving (and all vehicles), hostile flora, ammo magazines, flamethrowers, g.launchers, infinigun (the dual pistols)