There were no remaining Japanese military bases. We had either already bombed them, or they had dispersed or disguised them so we wouldn't. As one Army Air Corps official put it, "There are no more targets". Any further air attack would have been firebombing raids against major cities, more destructive than nuclear weapons albeit not as fast. Cities were bombed for the same reason that everyone bombed cities in WWII, to cripple the civilian workforce and affect industrial production and divert resources to damage control. Yes, they were deliberate civilian targets, that cannot be denied. So were London, Dresden, Hamburg, Coventry, Shanghai, Guérnica, and a host of other cities.

Hiroshima and Nagasaki were never bombed because they contained little military industry or bases, and consequently they were lightly defended. It also made them ideal "demonstration" targets. Tokyo and most of the other major cities were so heavily damaged already it would not have been very dramatic.

Dropping the bomb in an isolated area was actually considered, and rejected, because it would have meant first telling the Japanese it was coming to maximize the psychological effect, and if it failed to work, the effect would have been just the opposite of what they wanted.

And of course, what everyone forgets is that we only had two bombs, of radically different design. We had no idea either would work, certainly not both.

There is one other factor. By the time we made the nuclear decision, we already knew what the Japanese had done to our prisoners in the Phillipines, and to the Chinese, and we had seen what their allies had done to the Jews in Europe. We were in no mood to be merciful.