I can't see Injun resistance being much more than 'Indian Raid' events and negative provincial modifiers to represent raids and guerilla resistance to colonists. Perhaps colonising nations could choose whether to approach the natives from a trade and alliances vs assimilation and colonisation vs annihilation and genocide (forceful relocation?) perspective. My knowledge of history on this front isn't the strongest but as I understand this would be fairly plausible as you got things like the French and Dutch focusing more on trade and making a quick buck while the English and Spanish went for more substantial and long-term colonisation.
Tamoios Confederation, Tlaxcalla and others disagree with you. Injuns did manage to put some mean resistance from time to time.
EU3 handles natives that way - some events and genocide. Only few token native nations exist, and while they should be removed IMO they arent very problematic. The bigger issue is colonization.
In this thread there is more opposition to the idea than support. Paradox forums are not as stupid as you give them credit for.
The way colonization works is totally bogus too. Once you get to 1000 people, you get a city and magical cultural-religious conversion to your culture/main religion. I wonder why the Jesuits ever wasted so much of their time and money and manpower sending clergymen to America - They should've just waited until cities grew big enough, then the natives would've seen the glory of (insert nation/catholicism here) and collectivelly converted in a instant!
Teh problems with native american civilizations are two-fold:
1. European powers can bring as many troops as they want to America without any problem.
2. New World Natives can be easily annexed with conquest and enough troops.
2 could be easily fixed by making nomads (everyone except Maya, Mesomaericans and Andeans) provinces unconquerable, like Hordes but more... gradual.