Native tribes are just that: indigenous peoples that live on the maps where battles take place in Empire Earth II. They start off as neutral players and simply go about the business of building their own civilizations. While not that difficult to wipe out, the true strategy lies in making peace with them and bringing them in to your civilization. These native tribes hold the secrets to the lands they live on, and any player wily enough to make peace and ally with them will receive extremely powerful bonuses.
Your entire army can hit for much more damage, or you can research technology twice as fast! These bonuses are permanent as well--as long as the player keeps the native tribe alive. Such an advantage can easily turn the tide against any enemy, and it adds a whole new layer of strategy--past the standard "destroy anything that moves" type of thinking.
Sounds like they are using the same idea but doing it a bit better. I especially like the fact that the natives act like real people and build houses and hunt for food.