You think there were intellectual leaders like Fukuzawa who helped transition Japan from feudal / agrarian society into an industrial society.
Fukuzawa and many like minded intellectuals like him were indeed pivotal in helping shape Japanese educational system and learning of early modern Japan. It was intrepid men such as he that went abroad to learn from the west and brought it back to Japan and applied it to the Japanese context. I suppose the problem, my friend, is that while men like Fukuzawa helped to transform Japanese learning, in the core of Japanese society at the time, was still imbued with Imperialistic Ideology. Japanese society in that time was at a transitional period, so to say, very much like China of now; developing rapidly but still ideologically conservative.
Tho there were early Japanese state leaders who touted for Liberal Democracy, the time period was very archaic. It was a time of ideological warfare; we had the rise of Socialism , Marxism, Fascism, Democracy and Absolute Monarchy. In the pathway to finding the 'right' governmental methodology for Japan, I suppose the extremist imperialist radicals were able to get inside Japanese Government during this sensitive transitional period during the Meiji Era.
We had no advisers to help us find the right type of government; at that time there was no such thing as an 'NGO' or 'CIVIL RIGHTS GROUPS' , that was an era of Imperialism still. I guess Japan tried to adopt Western 'Imperialist Mercantilism' and went over board in the Imperialist ideology aspect.
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I like to think meta-analytically, my friend. I believe Nations are like people, and Nations make mistakes for a reason, and hopefully can learn from past mistakes. The goal is to learn from past mistakes and not repeat the same ones over , and over, and over again.