Bro, that NOVA was a joke! It actually in my opinion demonstrated all the more how LITTLE we ACTUALLY know about the period, and how much of a guessing game especially Meso-American linguistics is 
I guess you know much better than David Stewart, who was rewarded the McArthur Genius Grant at something like 17 years old for his understanding and advancement of the deciphering of the hieroglyphs, and subsequently taught at Harvard. How silly of me to recommend a brief overview to the layman when you are clearly such a genius! I should have instead insisted that you read book after book on Mayan linguistics, so that you could be certain that you know all there is to know, inside and out. Please, Habte, tell me then how YOU decipher ancient Mayan writings. I'm dying to know what you do that is so much more sound than the people who are already doing so.
The studies of Meso-American languages have no Rosetta stone, indeed, the guys in the 1960s and again in the 1980s were just about as making it up as were the guys before them. The guys today are a bit more sophisticated in their assumptions, however again, there conclusions could hardly be considered fact like say in Egyptology.
"Making it up as they go along", huh? I pity the students you teach, with that kind of attitude. You don't get a Ph.D. by making it up as you go along, or if you do, then I'm clearly doing this whole thing all wrong...
What happened in the Americas before the Spanish is in many ways as much a mystery today as it was ever. We have a of archaeological things we've found, but the Spanish burned all the texts
Except for the ones they missed.
There is a smug assumption amongst Western academia that they've answered all their questions, and indeed a lot of Mexican universities get caught up in these same fanciful assumptions. However, I respectfully disagree with a lot of their conclusions,
What definition of "respectfully" are you using when you accuse "Western academia" (who is that? I've never studied under "Western academia", just actual linguists, doing actual fieldwork) of smug assumptions? Nobody worth their salt working in ANY language is going to say that they've answered all the questions about anything. Please revisit the scientific method sometime.
Again, its not that I claim to know what happened in Meso-America, quite the opposite, all I am arguing is that we need to admit just how truly vague our substantive knowledge actually is.
That may be what you meant, but what you actually wrote was
"We might even be blatantly accused of CANNIBALISM!! With Meso-American history before the Spanish, we are essentially doing the same things." That is wrong. To say that knowledge is incomplete is one thing. I don't think anyone would say otherwise. To accuse entire (vague) fields of science of inherent bias, especially when the record of how the field developed is exactly the opposite of how you're framing it (i.e., it was
more biased/less evidence-based before, when people were claiming that the Mayans were all peaceful people) is something else entirely.
Anyone who pretend to know everything about what happened in Pre-Columbian Meso-America to any certainty is honestly either naive or just wishful thinking. There are a lot of books, a lot of studies, a lot of conclusions, but the evidence is stretched very thin and from an academic stand point, I truly question the integrity of the methodology.
First of all, nobody pretends to know everything about what happened in pre-Columbian Mesoamerica. Again, revisit the scientific method sometime. When you get to the part about knowing
everything there is to know about a topic under investigation, please let me know and I will adjust my own approach to research accordingly (probably by not doing it anymore, because what's the point if these other guys know EVERYTHING?). Until then, don't act like you're being even-handed, or are even the slightest bit interested in methodological integrity.