Why didn't they use their super AA to defend their cities?
Das ist eine gute frage.
Lets add it to the list:
Japan had pre war designs for standard escorts, but failed to mass produce them. Why?
Japan had the finest of 3 inch guns - something like our post war 3 inch 50 - but they had it EARLY - and failed to produce it in numbers. Why?
Japan a genuine political advantage in the anti-colonial sentiment in Asia - and (contrary to our assumptions and propaganda) Japan was NOT peopled or run by fanatics who had zero intention of empowering them. The Foreign Service was DOMINATED by such people, and TOJO himself was a big fan of their ideas - but Japan (with a few exceptions) failed to exploit this opening which would have made the autarky they sought a great deal more likely to come to pass. Why?
Japan was a pioneer in radar technology, and since WWII Japan demonstrated it had plenty of talent to teach and produce electronics of all kinds. But it FAILED to produce sufficient quality and quantity of radar during the war - often wasting years for the most marginal of improvements on captured or existing designs. Why?
Japan was not logistically oriented - in spite of the spectacular success of the Zaibatsu before and after the war. Why?
Japan had better intelligence than our other rivals in the great game. Japanese leaders were continually briefed about the status of the US Atom Bomb project, while the Germans were stunned we could make it work, in spite of limited success at the margins. The famous Russian intel on the same project pales beside the Japanese achievement of stealing samples of soil from reactor sites and stealing complete bomb plan sets.
Yet Japan failed to come to terms with what this would mean, if they didn't come to terms with us. Why?
The list is almost endless. There are specific answers to specific questions, not that we always know them all. But the general answer is that Japan was an extraordinarily divided society. Worse, it was an extraordinarily divided society with broken political institutions which had never really matured in the first place. "Government by assassination" may put a gang in power, but it does not give them strategic vision, nor political sales skills to sell that vision. What Tojo liked didn't matter when he was just a front man for a triumverate of generals who really ran things. By the time he got two of them out of the picture, his time was almost gone, and it was too late to change anything strategic - except maybe to kowtow and try to end it - something he was not up to doing. But Tojo was, in a sense you never read, an honorable man: utterly uncorrupt, a pioneer in aviation, someone the state could count on when very senior officers ran amok and needed to be reigned in, in more than one sense. He had very severe limits, particularly of what he understood, but he was not in it for profit, nor was he brutal, nor was he a lot of other things we usually assume or even hear. He was really just a fairly little man in a job utterly too big for him, with much less power than someone outside the system could appreciate, and he just walked away in the end. He went home to his family, and that is where we found him when the war ended. Doing nothing at all. With modest assets and habits. Japan was a nation dominated by a radical Army cabal that even ultra nationalists like Tsuji bemoan - one of the principle generals felt the critical decision was that to invade China - and he quit and said so - years before we got into it. That decision was NOT a proper national policy - but a decision made by a few generals NOT even in power and more or less forced on the nation over time. Japan was too divided and too dangerous to do things in a really organized and rational way.