Now, granted, it's hard to imagine a situation in which there exists in 2012 a sovereign and independent Iroquois Confederacy, but it's not at all beyond imagining that the Iroquois as a political entity might still exist in some coherent form.
Technically it still exists.
Anyway, colonial accounts pointed to large numbers of European colonists (not to mention freed Africans or runaway African slaves) immigrating into Indian territories and adopting Indian cultures. On a large enough scale, this could have produced mestizo/metis/maroon cultures, but ones which developed on an Indian base with European/African influence instead of ones which developed on a European base, which could be strong enough to resist concerted conquest and colonisation effort from highly organised and populous Western states. It will still be a very long shot, given the circumstances. I'm not not reducing Indians to "a feature of the landscape". I'm just stating that, in fact, European dominance was indeed assured given the circumstances.
I agree that the representation of colonisation in EU3 is a disgrace, though. I have started modding the game with the expressed intention of improving this.