This question is generally related to the Olmec, Aztec, Incas and Indian tribes in North America.
For such civilizations the greatest geographic challenge was their isolation from the rest of Europe and Asia where modern science was completely changing the world.
Also, these civilizations had abundant farmland, game and food supplies yet North America rarely saw the development of large cities which limited their progress in human development.
The civilizations you mention are not that early compared to most. But any civilization needs to have a secure food supply. So a geography that includes an area for good farming would be a necessity. Also, making sure the river you choose to live by is not going to dry up or freeze over every year.
