While more can always be said, there's plenty on atomic bomb targeting in this section of our FAQ. As a tl;dr, Kyoto was kept off the atomic bomb targeting list at the personal intervention of Henry L. Stimson, the Secretary of War; Tokyo itself had already been firebombed by the time that the atomic bombs were ready to use.

Tokyo had already been bombed in a massive firebombing campaign, mainly during Operation Meetinghouse on 9 March 1945, and days following. The resulting firestorm pretty much destroyed Tokyo more completely than nuclear bombs did Hiroshima or Nagasaki. Mostly thanks to the new B-29 bomber, which carried more payload further and higher. Making that bomber was the most expensive American project of the war, costing more than the Manhattan Project.

The B-29, the bombing of Tokyo, and the nature of creating firestorms with incendiary weapons are all complex, albeit ghastly. The greater capacity of the bomber is trivial by modern, jet standards but was impressive for the day at about 6 tons for that mission. Still, better results were needed, leading to the discovery that incendiary weapons caused much of the civilian infrastructure to add to the conflagration. The napalm and white phosphorus bombs caused numerous fires which spread, combining into a firestorm, in which massive heat causes equally massive updrafts ( causing the last bombers to struggle just to get over the target). This in turn, sucks in air from the sides, resulting in a storm-like effect over the city.

The difference (for the War Dept.) was it took over 300 B-29s doing multiple raids to destroy Tokyo. Hiroshima and Nagasaki took 3 bombers one trip.

For those interested, the specific raid has been covered in numerous places, but these books are a larger overview:

Wesley Frank Craven and 1 more The Army Air Forces in World War II (7 Volume Set)

https://www.amazon.com/Army-Air-Forces-World-War/dp/091279903X