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.
When beginning research on any topic, wikipedia is sometimes a good place to start. Wikipedia articles are sometimes the result of contributions by numerous well-informed people who care about a particular topic and who try to share their expertise with others. There are, of course, numerous potential problems involved in relying on wikipedia to any great extent: anyone can contribute to a wikipedia article; the editing can be done by anyone; changes can be made and then unmade; the article can be constantly in a state of flux; experts may actually be outnumbered, as contributors, by people who lack and expertise; etc., etc.
Nevertheless, having said all this, it certainly never hurts to take a look at wikipedia articles, because they often will point you in helpful directions, especially in their notes. The article that is relevant to your inquiry is here:
As you can see, in its present state (who knows how it will look tomorrow?), it needs further work. That's why it's good never to rely solely on wikipedia as a source of information. Many professors, in fact, forbid students to cite wikipedia articles, for all the reasons mentioned above.
When I searched for "Incas and Spaniards," the wikipedia article was the first thing to pop up, but many other articles popped up as well, and any search for information should consult more than just one source, especially if the one source suggested first by Google is wikipedia. If, for instance, you search in Google Books for "Incas and Spaniards," here is what you will find:
And, if you search Google Scholar, you will find this:
Never rely, then, solely on wikipedia. (That, at least, is my advice!)
One aspect of this that hindered them was the fact that they had no organized system for picking the next emperor after one emperor died. Not long before the Spaniards came, one emperor died of smallpox and a civil war erupted over who would be the next emperor. This left the empire weakened and divided when the Spanish arrived.
The Inca ruled a vast empire, encompassing over one million people. It was not really an Empire, but a confederation of tribes all of whom owed allegiance to a central ruler known as the Inca. The Inca himself was considered divine; so much so that when he was carried on a sedan chair, a servant accompanied him who caught the expectorant should he spit. His fingernail clippings were gathered and any discarded clothing was reverently and solemnly burned. Their religion consisted of a belief in a heaven, a hell and of a resurrection of the body after death. They made weapons of copper and bronze and ornaments of gold and silver. It was the gold and silver that attracted the Spaniards and ultimately led to the downfall of the Inca. When Pizarro captured the Inca, Atahualpa, largely through deception, he offered to release him if the people would fill a large room with gold and silver, which they did. True to form, Pizarro did not keep his word and had Atahualpa strangled, but only after he had been baptized as a Christian.
The Inca probably would have been able to easily overcome the Spaniards were it not for an internal civil war. Atahualpa's father had recently died, and a civil war erupted between Atahualpa and his brother who the father had favored to suceed him. Atahualpa had been considered something of a problem child. Atahualpa managed to depose his brother, but only at great military cost. When he met the Spaniards, he was in no condition militarily to oppose them, which led to his capture and the demise of the society.
An excellent description of Inca culture and society is in Charles Mann's 1491, New Revelations of the Americas before Columbus. I normally require my students to read it, and recommend it highly.