The reason Kyoto wasn't nuclear bombed in WWII was because the US Secretary of War had fond memories of his honeymoon there!
The U.S. government planned to drop more than just two atomic bombs in Japan during World War II. Groves, the U.S. Secretary of War planned on dropping one on August 19th, three more during September, and another three in October. That is a lot of powerful bombs falling on such a small island.
Groves sent Marshall a memo on August 10th saying to drop another bomb when the weather was clear sometime after the 17th or 18th of August. Marshall replied back that he wasn’t to drop another bomb on the island of Japan without express authority from the President. One of the extra atomic bombs would have been dropped over Kyoto, Japan.
However, the U.S. Secretary of War had his honeymoon there. He had such good memories of the experience that he didn’t allow them to drop a bomb on the city. What a nostalgic man.