Similarities:
Both conquistadors recognized and utilized the political crisis of the empires.
They both tryed their best to try and make the local populations obey then and they both imposed their own people.
Differences:
The Incas were a centralized government under the Sapa Inca which was centralized at the government at Cuzco.
The Aztec Empire expanded by means of getting rid of the current leaders and subjugated the local people.