Japan really wasn't in the same league as Germany Biggles. Germany was not only directly responsible for the war but it's governing structure was responsible for apalling suffering all over Europe. None of that could be feasibly left intact. Most of the people in charge were either killed in conflict, executed, committed suicide or were prosecuted for war crimes.
I tend to think that 3 days is a very long time in war to hold out before a second strike, especially if you have ulterior motives beyond surrender for making it. As to the first strike, well I go back to a past point. When an era loses so many people to war it dehumanises the living. I doubt there was much sympathy for the Japs and I completely understand why. And I'm sure the benefits off letting off those nukes were manyfold. That doesn't mean they were all the cause or rational for it.
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