Indeed, it needs rebalancing. Especially since native buildings are cheap, but greatly enhance provinces. It's like starting as European country with 2 tiers of almost free buildings available. Once you get 3/4 provinces upgraded, gold keeps flowing while your neighbours are still OPM moving around purposelessly. I'm fine with being a hudge blob by the time Europeans come to America with 10th of thousands warriors, I'll need it to survive, but it should not be that of an easy achievement.
A good start would be to just allow AI to form federations (I believe mine is the only one around and it is really a powerfull tool). AI should also use its colonists, perhaps with a decreased colonial growth attached to the native government type to avoid all of the Americas to be colonized by the time Europeans come in. That wuld help native AI catching up with a natie player and keep him in check at least for a while.
A good start would be to just allow AI to form federations (I believe mine is the only one around and it is really a powerfull tool). AI should also use its colonists, perhaps with a decreased colonial growth attached to the native government type to avoid all of the Americas to be colonized by the time Europeans come in. That wuld help native AI catching up with a natie player and keep him in check at least for a while.