So, this thread got me thinking and I decided to try and weird little challenge of playing a "historical" native council and not reforming government, which is essentially what the AI does. In the process I've learned some things.
Firstly, the AI can attempt to intervene in colonial wars. However, it is rare.
What the AI will do is to declare reconquest wars on any natives holding its colonial nation's cores. They will also declare their own conquest wars on occasion but they will declare those reconquest wars any time they can. Sometimes these wars can stall because of the AI shipping over tiny armies one at a time, but given the power of the colonizer nations they won't peace out and will eventually get round to sending 15k+ stacks which will wipe the floor with most native resistance.
Although the natives will confederate fast once the Europeans arrive, this can actually be counterproductive as it can result in very large but weak nations which will basically never get institutions due to the intrinsic native penalty.
The AI is not good at settling tribal development. A player choosing to stay as a native council has one massive advantage, they can develop land very efficiently while they catch up on tech by settling their tribal development, resulting in a much richer North America. The AI doesn't seem to do this very much or at all, even as a settled tribe. Presumably this is to prevent the megacities which were common in earlier patches, but it leaves them quite weak and low development.
So no, I don't think natives are overpowered. I think they're actually very difficult for a human to play if you play like the AI does. I'm sure there are games where the natives completely kick the colonizers out of North America, but I doubt it's happening on a regular basis. I think the AI's colonial expansion in North America might be slower than in previous patches, but that seems fine to me and is actually more historical.