Note that pretty much all of the North American megafauna were wiped out within a few thousand years of the arrival of the proto-Native Americans.

The only exceptions were species that were total badasses (bears, pumas), extremely prolific (deer), or a combination of badass and prolific (wolves, bison).

Also note that the pre-Contact Aztecs weren't exactly nice people. I believe it was Neal Stephenson who observed that one measure of how much the Aztecs sucked was that when the Spanish Inquisition took over, things actually became more humane.