Choosing Sides
After the first real stage, you'll have to make a critical decision, to align yourself with the Na'vi cause, or be a good soldier and stick with the RDA. This decision impacts not only what race you will play as for the rest of the game and specific missions, but most of the levels will be entirely different as well. If you enjoy Avatar, you'll definitely want to play both sides to see the whole game.
Humans
The humans are better armored and pack much better firearms. Hey have a range of weaponry to handle combat at various distances. The Standard Issue Rifle is a good, accurate, powerful weapon that can be very versatile. It's the weapon of choice for long-range shots, but suffers against faster enemies because of it's low fire rate. It is, however quite excellent against groups of Na'vi because of its heavy damage.
The Assault Rifle is fast and powerful, but not very accurate, and it can be quite easy to chew through ammo. You'll find it versatile against highly mobile enemies. The Shotgun is for close range combat, and can be effective against the Na'vi, but frequently goes underused because of its limitations. The pistols are best reserved for situations when no ammo is available, but they are reasonably accurate at least.
The RDA's ability set is a bit more limited than the Na'vi's, but still includes all the basics, like cloaking, healing, and the ability to call in strikes. One key difference is that the stat boost ability raises defense as opposed to offense.
The RDA's vehicles are a very nice perk. The Scorpion doesn't get a lot of use, but it's a powerful force. The ATV also packs a punch, albeit with limited ammo, and the Swan is deadly with two men to man it. The only shortcoming is the Buggy which, while fast, isn't as stable as riding a Direhorse.
Na'vi
You don't get to experience the real Na'vi moveset until after you abandon humanity. The Na'vi are much lower tech; you carry one gun, and it's not very accurate. Even more importantly, ammo for it is very limited. Instead you can use a variety of more primitive weapons.
The Na'vi have a higher learning curve in general. They favor melee weapons, which can be quite damaging, but leave you very vulnerable, especially since Na'vi defenses are fairly weak. The bow is a good longer range weapon that also has the ability to knock enemies down, but the low rate of fire makes it impotent against larger groups of enemies.
Because of these deficiencies, leveraging the Na'vi's special abilities is more important. They have the same speed ups, cloaking, and healing as the humans, but they also have a few handy abilities, like Titan's Bash, which stuns enemies, and makes using melee weapons more manageable. They can also summon Thanators for a ride and boost their attack rate.
The Na'vi mounts are quite different from the RDA vehicles, and not as well rounded. The Direhorse makes for a good, speedy, easy to ride means of transport, but like most Na'vi mounts, there is no means of offense. The Thanator is the best offensive mount, and even that suffers from very limited range.