savant,
I agree that the Iroqois represent the only solid bulwark against Euro expansion in North America, and thus should remain.
In fact, if people are upset that the Iro are too weak, then perhaps increasing their territory to include some of the Eastern Great Lakes (the Upper NY and lower Ontario region). A bit ahistorical, but reflecting the fact that they, along with the Huron, agreed in one thing, stopping the white man from destroying their way of life. This would slow down colonization a bit more, and thus also put the development of the North American colonies a bit more on a historical timeline.
State,
I like your idea, I think it is a good compromise actually given the game engine's setup right now. Perhaps give the Iroqouis a temporary CB against England in the 1750's to represent the rising tide of anti-"Yankee" sentiment among the Indian tribes. The French and Dutch, it seems to me, already have a better chance of colonizing provinces in Indian territories. So there is some reflection of historical Indian relations in the game engine already. This would seem to be a logical step from that. If the English aren't around, the Temp CB won't hurt, because they won't be able to reach them anyway. If they are, it serves to increase English discomfort in the New World with the natives (historical event) and increases the likelihood that the English may lose some NW provinces on the Eastern seaboard and trigger the Independence Revolt, thus satisfying some of our desire to see the US come into being.