Why not Tokyo? Why two smaller cities, and why those two specific cities?
The Americans came up with a short list of targets that had both some military value and had not yet been bombed. They also wanted targets with no complicated geography (ie, not spread out over hills). Finally, they wanted targets that would produce devastating psychological impacts. Overall, this meant military targets in flat urban areas that hadn't been bombed. They treated the bombings a part military operation, part scientific experiment.
Jones, Vincent (1985). Manhattan: The Army and the Atomic Bomb. Washington, D.C.: United States Army Center of Military History
Also, the city of Kokura was one of the primary targets, but it was too cloudy in the skies over Kokura both days of the nuclear strikes, so it was spared.
Tokyo was out because it had been bombed flat in repeated raids, so there wouldn't be a huge amount of additional damage that the bombs would cause, even though it would cause a much greater loss of life.