I haven't been to Nagasaki but I can comment on what I liked about Hiroshima. I thought it was a beautiful small city. It's on a river delta so there are lots of bridges on river crossings, which makes for nice scenery. You can take boat rides, or walk along the pathways next to the river. If you're lucky maybe catch a music performance or night illumination/art show, though I suspect this might be a seasonal thing.

Being around the Peace Park/Atomic Dome/Museum at least for me was quite overwhelming, having the river nearby had a bit of a soothing effect.

And also echo evergrn's comment, Miyajima is very pretty. I only had time for a half day there, but people recommend staying on the island overnight.