Colonization 2071 allows you to play natives, though they renamed them to aliens. As already mentioned, a whole lot of features are disabled for natives, which are enabled in col2071 or playing aliens would really suck.
I don't think that is what you had in mind, but I think that is what is currently possible. I once tried playing natives in RaR (I had to modify XML to do so) and I didn't even manage to finish the first turn without the game crashing. It's simply not designed to handle human inputs to natives.