The targets were mid-sized cities because by the time the target planning started, Kyoto was the only big one the B-29s hadn't burned to the ground (well, the important parts; I forget when, but we'd given up on Tokyo after destroying 17 square miles or so), and Secretary of War Stimson, who'd visited it and Japan in general, removed it from the list, despite Groves imploring him many times to not. That was wise, if for no other reason that it strengthened the Emperor's hand when he was finally in a position to end the war, for a long time Kyoto was the Emperor's city, Tokyo the military's.
The targets were mid-sized cities because by the time the target planning started, Kyoto was the only big one the B-29s hadn't burned to the ground (well, the important parts; I forget when, but we'd given up on Tokyo after destroying 17 square miles or so), and Secretary of War Stimson, who'd visited it and Japan in general, removed it from the list, despite Groves imploring him many times to not. That was wise, if for no other reason that it strengthened the Emperor's hand when he was finally in a position to end the war, for a long time Kyoto was the Emperor's city, Tokyo the military's.