No they are not "completely different" at all. Unless your version of North American history begins with Francis Cooper's Leather Stockings and the French and Indian wars.
North America had lots of towns and cities in the time before the European arrival. In fact the first European explorers of the North American shores actually reported that the coasts of, for example, New Jersey and Virginia were densely settled and that the landscape was quite thoroughly cultivated by obviously sedentary people. The Mississippi valley and the Ohio valley were home to settled civilizations centered around large towns with huge ceremonial buildings. (The mound builders.) These civilizations had spread all the way throughout the southeast of the US, where the 1539-1543 expedition of Hernando de Soto encountered a fairly densely populated region full of towns.
The civic "memes" of these civilizations were quite similar to the mesoamericans: They were centered on towns, made a living off intensive agriculture and long-distance trade, maintained powerful priestly castes who ran much of the civil organization, and they dedicated immense efforts towards the construction of landmarks. Obviously the mesoamerican peoples were technologically more advanced and had in general more people living in their cities, had more social sophistication and made more ambitious conquests when they went to war. But as far as archaeology and the few sources can give us an image of the north american civilizations, these people weren't hugely different from the mesoamericans.
This is the world in which a pre-"discovery" native American experience should take place. Not this farcical last-of-the-mohicans-themed, peace-pipe-smoking joke of a mini-game.