Clearly the belief in their own innate superiority and the god-like status of their ruler was a major factor that helped the Spaniards greatly. Underestimating the invaders was a key mistake that cost them tremendously, as was the religious belief that their ruler was their religious deity.
The disorganization was a feature of not having a complex enough government structure or sophisticated enough weapons. There was also an empire extended too far, which is commonly the cause of an empire's downfall when invaders come.
Also consider the Inca road system; it was one of the first true highway projects in the world, and much of it came from existing roadways annexed by the Empire. It allowed large-scale, reliable transportation of people, livestock, and food from all over South America. It was primarily a footpath, since there were no horses. When the Spanish took over, they unintentionally destroyed most of the road with their iron wheels and horseshoes.
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