In general, I do agree with Diamond's argument in Chapter 3. He argues that guns, steel weapons, horses, infectious diseases, maritime technology, centralized political organization, and writing all helped the Spanish to conquer the Incas. This is a very comprehensive list and it is hard to argue with any of his statements about how each of these things was important.
However, we are left to wonder if there are factors Diamond did not include. Diamond says, for instance, that the lack of writing caused the Incas to be more ignorant of the Spanish and of a "huge body of knowledge about human behavior and history" that the Incas could not access because they were largely illiterate. But what if their illiteracy (and possibly the gullibility that allowed them to trust the Spaniards) were caused by them having an "inferior" culture? What if their religion in some way encouraged them to think less and to believe more in supernatural things (like Europeans might have before the Renaissance)? These are cultural factors that might have helped to make the Incas weaker than the Spanish.
So, I cannot argue with anything Diamond says to explain the Inca defeat, but I wonder if there are other factors that might also have been relevant.