Nagasaki >>>>>>>>> Hiroshima. Not even close.

The problem, of course, is getting there. Nagasaki is clear down on Kyushu and even when you get there, it is several more hours by train from Hakata (Fukuoka.) Being a bit of a train testu, I used my Rail Pass to go all way from Nara in one day and then, on the return, stopped at Fukuoka for several days to see the rest of Kyushu after Nagasaki. The run back to KIX from Fukuoka wasn't too bad on my departure day. I would recommend at least 2 and better yet 3 days for Nagasaki.