From what I understand, the reason Chakotay is a bunch of stereotypes is because Michael Piller and Jeri Taylor got taken in by a con man who presented himself as a Native American expert, instead of them going out to recruit actual academics.
They didn't need to talk to academics. All they needed to do was talk to some real live Indians living in the 20th century. Pick a tribe, any tribe. Want to go with Mayan, as Beltran suggested?
All they needed to do was talk to their gardeners.
Well, if I recall correctly, the con man who advised the Voyager staff on Chakotay's character got the job by presenting himself as an Indian. At least with an academic you can get people to look into their credentials and even better, they probably knew actual Indians the writers could talk to.