When it comes to trains with characters and personalities, JR Kyusyu does it best out of all other JR companies. JR Kyusyu Trains Although I think many private rail companies in Japan do better than JR. I really do think after all these years JR still cannot rid of old government entity days. Limited Express Kamome uses 885 Series train which was one of original “unique train” JR Kyushu made.

Nagasaki is a nice place, definitely recommend that. Nagasaki has a street car (PDF file) which take you around the city. As other have mentioned, maybe only drawback of Nagasaki is distance and time take to get there especially if you are traveling by train.

But Hiroshima is nice place also, you will not regret if you choose to visit Hiroshima. A lot of pretty small islands in Seto Inland Sea, Miyajima as one of most famous. Can easily take a train inland and have a view of mountain side, which I did, took train to Sandankyou (today Kabe line terminate at Kabe and does not go all the way to Sandankyo which is a picturesque gorge) and Geibi Line to Shiwaguchi. Riding along country side on local train. Don’t forget, Hiroshima has a street car, too!

If you are going to be in Osaka/Kyoto area then as a train geek recommendation will be Umekoji Steam Locomotive Museum in Kyoto.