The shinkansen as far as Hakata is pretty much like any other Hikari or Sakura "bullet train." Some interesting scenery but it goes by pretty fast. For me, it is a good chance to enjoy an eki-ben lunch box and catch up on writing for my e-mail/photo blog. It'll take a little over 2-1/2 hours from Shin-Osaka Station. If you'd be leaving from Kyoto, you'd have to take a train to Shin-Osaka and change there.

From Hakata to Nagasaki, you would take the Limited Express Kamome, which will take just under 2 hours. That run down the western edge of Kyushu is much more scenic.

Once in Nagasaki, the best way to get around is the tram system. Get a pass and route map from the Information Center at the station or from your hotel. Most will have it.

There are many, many interesting and historic sites in Nagasaki so I'd recommend some research, or better yet a guide book. There is much to see and it is spread all around the city. I liked the atom bomb museum better than the one at Hiroshima. It is underground, under a glass geodesic dome, which is pretty cool, and is very complete if somewhat compact.