I know I haven't done much of what I said I'd do for this mod, but I have now assembled a full cabinet for the Inca Empire at the time of the Spanish conquest- I was thinking perhaps the situation with the Inca and Aztec Empires would be similar to that of Italy and Ethiopia in the very early years of HoI2 vanilla- a quick, tough campaign for the Aztecs and Incas- but with one difference- the Spanish are outnumbered, even though they have far superior technology.
Also, to stress the difference between the two Empires, I think the Aztecs ought to be an alliance of four different nations (as the Aztec Empire originally was, I believe) in order to show the relative weakness of its central government- or lack thereof- compared to the Incas, who won't be a pushover.