One question I keep posing myself after reading this post: the Aztec empire came into contact with the Spanish around 1520. The Japanese empire came into contact with the Europeans around 1600. The Aztec empire fell within weeks. The Japanese managed to give the Europeans just enough to keep them from mingling in their affairs until they famously 'pulled a Meiji'.
So what was it that Japan had that Mezoamerica didn't? Was it steel? Horses? Widespread literacy? Did it just come down to geography: Japan being an island or being close to China and Korea? Or was it just lucky to get involved with the Dutch and Portuguese rather than with the Spanish?
Or was it just bad timing that Cortez hit the Aztecs at just the right -or wrong- time when they had a simmering civil war just waiting for a spark?
Or did, like Jarred Diamond famously wrote, in the end it just came down to guns, germs and steel. And if so, if the Aztecs had at least two of these themselves: guns and steel, or steel and (resistance to) Germs, would they still get conquered?
Japan was fairly politically unified. Even during the Sengoku Jidai, everybody still paid nominal fealty to the shogun and emperor. Look at how swiftly Hideyoshi organized a coordinated invasion of Korea barely 2 years after assuming power.
Mesoamerica was not. Even the Aztecs were a collection of city-states closer to a confederation than a modern nation-state, and they made a lot of enemies in their conquests, who would eagerly help overthrow the Aztecs.
Also, the Aztec timeframe is off. First contact was made with Juan de Grijalva in 1518, and even Cortes only launched his expedition in 1519. It took more than a year for Cortes to conquer Tenochtitlan after fleeing during
La Noche Triste.
Ultimately, I would say most of the legwork was done by Cortes' native allies that had various grievances with the Aztecs. After all, the Aztecs were actually outnumbered in the siege of Tenochtitlan. The Spainards themselves weren't actually that large of a force or even that well equipped, given that most of their horses and artillery were lost in
La Noche Triste.
Specifically regarding disease, the smallpox epidemic did start in 1520, but I think the epidemic was too recent to have significantly effected the conquest of the Aztecs. On the other hand, the Inca did fall into a civil war because of a smallpox epidemic, making Pizarro's job a lot easier.
So Japan had the advantage of relative political unity and disease resistance over the Aztecs. Another advantage Japan had was that the Portuguese were already humbled, losing several battles to the Ming. As a result, the Portuguese adopted a more mercantile approach with Japan instead of a hostile approach like they did with Malacca and Goa.
Needless to say, I have a lot of issues about Diamond's tale of the conquest of the Americas.