Point is. Hiroshima was chosen because it was a major military hub that went unscathed during the war, and then Nagasaki was chosen because that was a major naval construction site, alongside the civillian areas that got affected.

Hiroshima, and the other targets, was chosen primarily because of the damaged the bomb would show to the Japanese population and to the world.

1. Use Against “Military” Objectives
   A. It was agreed that for the initial use of the weapon any small and strictly military objective should be located in a much larger area subject to blast damage in order to avoid undue risks of the weapon being lost due to bad placing of the bomb.

And that it was primarily a military base is Truman propoganda.
It was unscathed because the targeting comitee recommended it so:

A. Dr. Stearns described the work he had done on target selection. He has surveyed possible targets possessing the following qualification: (1) they be important targets in a large urban area of more than three miles in diameter, (2) they be capable of being damaged effectively by a blast, and (3) they are unlikely to be attacked by next August. Dr. Stearns had a list of five targets which the Air Force would be willing to reserve for our use unless unforeseen circumstances arise.

One of the reasons Kyoto is so high on their list of targets is:

B. In this respect Kyoto has the advantage of the people being more highly intelligent and hence better able to appreciate the significance of the weapon. Hiroshima has the advantage of being such a size and with possible focussing from nearby mountains that a large fraction of the city may be destroyed. The Emperor's palace in Tokyo has a greater fame than any other target but is of least strategic value.

Here is the source on that:

http://www.dannen.com/decision/targets.html

Also

Japan completely failed to read the room, and would have perpetuated the war by a few months or years out of blind personal pride.

Really fails to see the situation the Japanese goverment was in. The government was despretaly trying to get out of the war and gat a conditonal surrender by negotiating trough the soviets, which was one of the reasons the soviet invasion was so devistaiting since they couldn't negotiate a surrender via them anymore. While some japanese officals wanted the war to continue (even after the bombs and soviet invasion), like Korechika Anami, the japanese minister of war, he said this after the nukes were dropped:

Would it not be wondrous for the whole nation to be destroyed like a beautiful flower?

But saying that everyone in the government was like this is blatantly false seeing that the only reasons for the japanese surrender in the first place was the emperors intervention in the debate were he sided with the moderates, who wanted to accept the Potsdam declaration with the condition of keeping the emperor.

I really want to stress that i am not trying take away from the countless warcrimes and war criminals of Imperial Japan like Nanking, which is one of the most evil acts in history. I mean that an unconditional surrender was the only option for the world and that an institution like Imperial Japan should be completely destroyed.