The TC beta rule is a killer for a lot of states, not just the exotics.
Slowing down exotic tech growth in the military sphere may make the fall of the Incas more likely, and the Chimu might even vanish - only eliminated by the AI in one my GCs, and that was Colombia in the 1800s.
It's tough to get a balance between the historical reality of the native American powers and the game play issues. The Iroquois are a fun power to play as it stands now, but I wonder how they can fight a war at all now in the betas. No census tax without infra1, and now no trade income from the absent Manhattan CoT if they get to trade1. Removing the maintenance costs for exotic armies is an interesting option, but then you'll have armies of 100,000 Huron warriors if they build 1000 every year until the French show up.