When I was in Peru I couldn’t believe that the Incan sites we visited weren’t far older than they are. With no intent to be disrespectful at all, it seemed like in some ways the architecture was way behind what was going on in Europe at the same time. And when the Spanish came, the Incas didn’t have the weapons or defended that needed to fight back and were essentially overrun. So my question is, what were the Incas doing while different European countries were developing navies, fortresses, and weapons? What was their focus on if not those sort of things?
I'd ask you to consider why you think Inca architecture or defenses were "behind"?
The Inca empire had extensive networks of fortifications, but they were mostly located on the imperial frontiers by the time of the Spanish invasion. The Inca were also capable of mobilizing large armies (the Chronicles say up to 30,000 men, though thats probably an exaggeration). These armies weren't made up of full time professionals, but neither were most European armies until the 17th century. Inca weapons, largely slings and maces, were simple. They were nevertheless well adapted to a system of Andean warfare that focused on, among other things, prisoner taking and hilltop defensive positions.
It wasn't that Inca forces were woefully underdeveloped or were caught unprepared because they happened to be focusing on other things. The significance of technological advantage in the form of gunpowder or steel, I would argue, is frequently overstated. What was much more decisive in terms of Spanish victory was timing.
Pizarro's invasion happened to be timed perfectly. The Inca were just emerging from a civil war, and different ethnic groups within the empire, including the Chanka, Cañari, and Chachapoyas were eager to ally with the Spanish in order to throw off their Inca overlords. Even then, the newly victorious Atahualpa's forces could've wiped Pizarro and his men out at Cajamarca had the order been given. Perhaps overconfident following a string of victories, Atahualpa made the decision to agree to an audience. Pizarro then followed Cortes' example to the letter, took Atahualpa hostage, and the rest is history.
It is not however, history attributable to divergences in some sort of evolutionary trajectory. Rather it is history as created by one fateful decision made in a larger context of Andean political instability.