lumpthing
generic lump
The Iroqouis would fit the bill alright, since they did expand (immensely) after the arrival of the Europeans. English guns greatly accelerated their conquest of native rivals and, for a time, they went from controlling a small patch in upstate New York to dominating much of the Great Lakes basin. And they were never really trying to drive off the Europeans ... they were very close partners with the English and sought to - well, did - achieve a standing in North America equivalent to any of the colonies. Until the Revolution, when they disintegrated in internal divisions over questions of which side to retain allegiance with. I think this group, at least, would fit well in the context of the game.
The other groups might be difficult to portray, though.
I think the Aztecs and the Incans would be good as well. The Spanish were very lucky with these two great empires. The Aztec king decided they were prophesised gods and refused to fight until it was too late and the Incans were crippled from their civil war (and possible thought the Spaniards were gods too, I can't remember). If it wasn't for these two accidents of history, those nations might still be with us today.
If it was to have basis in history then playing as the natives would certainly be more of a challenge than playing as the Europeans, but what's wrong with that? I'm disappointed it isn't possible to play as any native civs, but I'm sure it will appear in the mods.
I can understand why some people might disapprove of a game about colonization because colonization did go hand-in-hand with racism historically. However that's true of just about any warfare-based game (and that includes non-European wars). It's only in modern times that there has been a significant movement against denigrating other cultures.
Also, historical colonisation involved good motives (a free-er society, greater knowledge of the world) and neutral ones (more trade) mixed in with the evil ones. Colonisation cannot be reduced to just a racist ideology and nothing more. For me what made Sid Meier's Colonization fun was the excitement of discovering and settling an unknown land and the way that instead of generic 'hammers' and 'trade' points you had actual resources and manufactured goods, transforming the civ economy into something more meaningful and playable. I think this reflects how Colonization was more than conquering and ideologically degrading native americans.
Finally, the player doesn't not have to oppress the natives in Colonisation. They can trade with them give them gifts and always be nice to them.
None of that applies to Grand Theft Auto, where the player can only follow the 'evil' path and has no better in-game motive then self-advancement, but which this blogger guy apparently didn't criticise.