I am smitten with Nagasaki -- such friendly people, an incredibly scenic city, and a lot to do! In terms of A-bomb stuff, I found Hiroshima more memorable overall, although IMO the Nagasaki museum is more impressive.

If you have time to explore the surroundings, parts of Kyushu are beautiful; Mt Inasa has amazing nighttime views, Battleship island is fun, and Huis ten Bosh provides a glimpse at bubble-era Japan madness.

My only gripe is with getting there; I'm not much of a train buff, but I enjoy the Shinkansen as it speeds along. Sadly, it's mostly tunnels east of Osaka, so the trip gets monotonous. And the Kamome Limited Express from Hakata to Nagasaki is a slow, bouncy affair. I'd fly (peach to/from Osaka or JL ... well worth 4.5k Avios to/from Tokyo).