I guess that if Leugi is ok with lumping all the South American countries into the Colonial group, it should be ok.
Technically, Peru, Bolivia, Argentina, Uruguay and Chile are one kind of monster, while Paraguay, Brazil, and to some degree Colombia, Venezuela and Ecuador are another kind of monster. (Colombia and Venezuela stand in the middle ground of both, though Colombia is even more related to Central American countries); and of course all are very different to Anglo-American countries.
However, it's hard to give a major difference between them for the game, mostly because they are also very modern.
Andean American modern Countries have had a lot more interest on Archaeology and ancient cultures than Amazonian Countries, but far less so than Central American countries. So its not only for them... Amazonian Countries have a lot more natural resources, but Andean American tend to focus on other kind of resources too (like Guano or Saltpeter)... They all tend to be very syncretic, mixing religions, and they all had troubling politics dealing with dictatorships and ugly things like those... So, the differences are more individual than group-like...
Withouth thinking in Gameplay, the American Continent could easily have: Andean, Amazonian, Mesoamerican, North American (native); Latin-American, Anglo-American (North) and Caribbean... But right now none of the groups would even reach 8 civs...
I'd be in favour of sepparating Latin-American (including Mexico) with Anglo/French-Colonial (Like USA, Canada, etc) [though I have no idea on major differences either]... I wouldn't know where to put Philippines, don't know much about them...
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I will start trying to figure out how to deal with Northern-Tribal American, Amazonian and Andean Culture groups little by little... Once I get some ideas (probably helped hugely by turing and reedstilt) we can touch this issue betterly.