Let me try to analyze it more historically for you Fawr here is basically why I say that historically the way the conquest happened was very unlikely.
All the following happened but most historians on the period would agree that Cortez was one of the luckiest people alive.
1) Spanish happened to look like and arrive at the exact date of the arrival of the god Quetzalcoatl. While the nobility might not have believed that he was a God many peasants would have and thus this would have lowered moral amongst their men.
2) Had Moctezuma II Xocoyotzin NOT been a warmongering powerful emperor and instead been a leader who solidified power he would not have had such an unstable realm. He had just conquered the Maya city states of Xicallanco and all the city states around Tapachula (near border of Mexico and Guatemala). The conquests of all this land in the south and all the Maya lands outside of the Yucatan Peninsula led to a lot of rebellious provinces under his control. He also went to war against the Tlaxcala, Huexotzinco and the Tarascans which were the Aztec's major enemies of the time.
3) This warmongering and vast amounts of sacrifice that he demanded to celebrate his victories which culminated in the 1487 sacrifice where somewhere between 10,000 and 80,000 people were taken from tributary vassals and sacrificed. This led to the Aztec's vassals and tributaries resentful to the Aztecs so when the Spanish arrived all the east coast vassals defect and join the Tlaxcala-Spanish Alliance and overthrow their Aztec's overlords. They decided at least the Spanish overlords would not be as bad as the Aztec overlords. Had this not happened Cortez would have gotten few allies and not stood a chance vs the hundreds of thousands of Aztec warriors with only a thousand men. In addition had Montezuma taken the Spanish as a serious threat from the beginning he would have just ordered his army to go to the coast and crush him before he even got inland and thus he would not have been able to get native allies. Montezuma had Cortez monitored but never interfered with, had he just immediately ordered their death (which many generals wanted to do) he would have surely defeated the Spanish with overwhelming force or at least scared them off.
This is why I am saying that without many events coinciding the Spanish would not have been lucky enough to have the Aztecs in an unstable scenario when they beat them. Disease would come only after the Spanish had already gathered an army and started open warfare with the Aztec. Had the Aztecs not created a perfect storm of procrastination to deal with the newcomers, disbelief in the Spanish being an actual threat (After all who would have believed that a thousand men could defeat an empire of millions), pissed off all their non heartland vassals, and been at war with their neighbors the Spanish would have had a much harder time using divide and conquer to defeat the Aztecs.
With all the above taken into account I STILL want Iberia to have large colonial empires in EU3. What happened historically should be likely in the game BUT I want to stress how unlikely all these things were in real life. Because they were unlikely in real life I want to make it so that Natives survive say a 1 in 10 times. I am NOT SAYING that natives should survive intact as native cultures non westernized, pagan, etc. I am thinking a Japan scenario where the nation quickly recognizes Europeans as a threat and as superior and they quickly westernize and survive as a Hybrid native/western nation.
The Inca account is even more ridiculous. The Inca Emperor, heir, and next heir all died from disease simultaneously thus leading to the next two sons going to war with each other in a North vs South war, and then the son with LESS backing won thus leading to a government of low legitimacy, instability, and a severely weakened army with little loyalty to the central state. The North side won but then the Spanish invade from the north thus defeating the Emperor's loyal people first and then the central areas of the nation side with the Spanish to get back at the North which had just conquered them. It would be as if in the American Civil war ends, then Great Britain invades New York and the South immediately again declared war and joined the British against the Union. If a human was controlling the Inca perhaps he could win the civil war faster or at least have it so the larger portion of the empire wins the civil war, or maybe he could just have some luck and not have all 3 parts of the national succession did not simultaneously die.
There is that enough historical analysis for you? If you want a good book on the Inca conquest I suggest
http://www.amazon.com/The-Last-Days-Incas-MacQuarrie/dp/0743260503 it is easy and enjoyable to read and gives the tale of the conquest from a non partisan point of view. Showing both sides and how the Inca came very close to pushing the Spanish out in Manco's rebellion but failed in the end. Manco sent soldiers to Lima under general Quizo Yupanqui who defeated the Spanish three times in the Andes but was defeated by a combined Spanish and traitor army at Lima. Manco himself was defeated and failed his siege of Cuzco, though he retreated to Ollantaytambo and won a battle there he had lost the war.
Joe as far as revisionists go...do you actually believe the primary documents that the Spaniards sent back to the King? The Spanish accounts blatantly lie in half the accounts multiplying native armies by about 10x and by pretending that they had NO native auxiliaries. According to the Spanish they went alone with no allies and crushed millions with practically their bare hands. They also have no one to verify their stories they are trying to glorify themselves so that the King will reward them more (which he did) so we have to see both sides of the story to get a true portrayal. I hate people who are revisionists just to be revisionists but in this case I believe that you just cannot believe the primary documents completely. I want to agree with you Joe I am Spanish by descent but I simply do not see the evidence to support Spanish claims to everything they did. I want Europeans to conquer the natives most playthroughs 9/10 times if not more BUT I want it to be so that natives get a chance to actually fight and be much more fun to play than they currently are.