Of course with taking out those two cities we had taken out much of Japan's ability to rebuild.
The other three cities that were considered for atomic bombing were Kyoto, Kokura and Niigata.
Quoting from my senior thesis:
When Secretary of War Henry L. Stimson was shown the list of selected targets, he immediately focused on Kyoto. Stimson was adamant that it be removed from the target list. Groves explained that it would be the best target because of its large geographical size and population of more than one million. This would allow for easy measuring of the blast effects because it was so large and not separated by any significant bodies of water. Kyoto also had a large industrial infrastructure that was without doubt producing war materials. Nevertheless, Stimson was not going to allow Kyoto to be used as an atomic target. “The reason for his objection was that Kyoto was the ancient capital of Japan, a historical city, and one that was of great religious significance to the Japanese.” (Groves 1962, 273-274)
Even though Stimson had put Kyoto off limits, Groves continued to attempt to persuade him otherwise. While Stimson was at the Potsdam conference, Groves tried yet again to have Kyoto designated the primary target. The message that came back, this time from President Truman, stated Kyoto would not be touched. That telegram saved Kyoto from any risk of being an atomic target but almost caused it to be burned to ashes by conventional fire bomb raids. With Kyoto removed from the list of atomic targets, it was no longer protected from General LeMay’s B-29's which were starting their fire bombing campaign against Japan. When General Groves realized this, he contacted General Hap Arnold who insured that Kyoto would technically remain on the target list even though it was no longer being considered for atomic attack. (Groves 1962, 274-276) A replacement was needed now that Kyoto was removed from the list of targets. In its place, the city of Nagasaki was chosen but as a Class B Target. (Groves 1962, 309-310) An irony of the Manhattan Project is that it developed and deployed a weapon that could destroy a city with a single blast but in the process saved Kyoto and several other Japanese cities from destruction by B-29 fire bomb raids. Every city on the list would survive the war except the two destroyed by the atomic bombs.