I recently read the book 1491 by Charles C. Mann; a survey of more recent thought on the state of things in pre-Colombian America (as well as a fair amount about historiography).
Short version: Yeah, there were a lot more people and civilizations than you'd think. No, more than that. Basically huge chunks of the landscape all over the place were formed or influenced by the various native cultures living there, and for a lot of places the first detailed accounts we have from European explorers is from generations after 90%+ of the previous population had died off from apocalyptic epidemics and most of their systems had collapsed and everything had gone to seed and been overgrown.
For instance: Huge primeval forests everywhere in eastern North America? Nah, there were a lot of farmlands and a lot of managed forests. Then the farmers died and stopped managing the forests, sp everything got overgrown. Huge herds of bison roaming everywhere? Nah, the herds used to be smaller and more limited in distribution; the farmers wouldn't want their fields full of bison, but they would want to have some reasonable herds available within reasonable distance so they could go on hunting trips on a regular basis. Then the farmers died and stopped culling the herds, so their population exploded all over everywhere. Amazon rainforest, untouched primeval jungle? Not so much, there's evidence that a lot of the (rather nutrient-poor) soil of the region has been improved and used for long-term farming and fruit orchards. Then those farmers and gardeners died and things grew wild. And so on and so forth.
Also all of the natives that we have any sort of records about are known to have had heaps and heaps of their own internal and external politics which typically got exactly as complicated as those of all other human cultures we know anything about. And presumably the same would have been true of all of those natives we don't have records about. They got handed the rawest deal in history with all of those apocalyptic epidemics that were followed up by aggressive colonizers, but this does not mean they were passive victims with no agency of their own. The usual pattern that allowed colonizers to take over was not simply an exploitable instability due to e.g. one of those apocalyptic epidemics, but this in combination with some local factions deciding it was in their best interest to cooperate with these new foreigners in order to gain an advantage over their real enemies (and sometimes they were even right in the short term).
