To make playing as a native American more interesting before Europe arrives, it seems to me that making the two or more province natives use their colonist very aggressively would be beneficial. I assume that the reason they don't is to leave provinces open for Europeans to use colonists on once they arrive, but I have a suggestion that may allow us to have our cake and eat it, too:
Once Europeans start colonizing the new world, each native nation should start losing provinces to disease. Tie these province losses to events so that human-controlled natives can have some influence over which provinces they lose and/or how quickly. Coastal provinces should be the most at-risk, with inland provinces enjoying a small measure of protection. You could also use these events to free up some of the insane glut of gold natives usually end up with; perhaps province-loss events should be able to be staved off with massive gold investments (to the tune of 500-1000 gold/province).
Of course, capital provinces should be immune to loss, although perhaps coastal capitals should still have negative events tied to the influx of disease via temporary production and tax efficiency losses.
Once Europeans start colonizing the new world, each native nation should start losing provinces to disease. Tie these province losses to events so that human-controlled natives can have some influence over which provinces they lose and/or how quickly. Coastal provinces should be the most at-risk, with inland provinces enjoying a small measure of protection. You could also use these events to free up some of the insane glut of gold natives usually end up with; perhaps province-loss events should be able to be staved off with massive gold investments (to the tune of 500-1000 gold/province).
Of course, capital provinces should be immune to loss, although perhaps coastal capitals should still have negative events tied to the influx of disease via temporary production and tax efficiency losses.