I deliberately gave the "if you were a chieftain" example because spontaneous reorganization is almost as difficult as making your enemies spontaneously nicer.

And I deliberately gave the example of Japan. I don't know enough about Native Americans to say exactly how I'd go about the equivalent of a Meiji Restoration, but that's what I would attempt. I'd pass laws mandating compulsory Westernisation, forcibly settle the nomadic peoples, do my best to Christianise the country, and try and import as much technology and Western practices as I possibly could. And naturally I'd try and crush my rivals to make sure there was no alternative plan. I'd have tried to make Western contact as much of an opportunity as possible - Western imperialism was the best thing that ever happened to the country my family are from.

Also there are examples from history of colonized people who suffered less than others

Definitely so. The ones who suffered less are generally the ones who adapted. There is no alternate history where a nation of nomadic hunter-gatherers are wandering the Great Plains hunting buffalo in 2014. And frankly that would have been a pretty miserable outcome even from the Native Americans' perspective. Unfortunately, it's that rather romantic vision that inspires, rather than a more pragmatic one of a rich and populous Native American nation, but which is culturally not much different from its "American" neighbours.