Yes, I have already created events that will guide the A.I. into conquering the Incas. But there are other ones which needs work, like the Lenape, Huron, Navajo, Maya.. etc. I would deal with them, but I don't know much about the details of them.
I think it would have been far less of a problem if the provinces in the Americas were made alot smaller. This would have allowed colonies to be constructed, without having the natives covering up all the territory. Another potentially nice idea, would have been to be able to kick the natives out of a provinces, then they would move into the nearest uninhabited province. But these ideas, if ever implemented, will have to wait until EU3.