First, if by "walking the less traveled paths," you mean "hiking around", I'd recommend picking up (if you can find a copy, it seems to be out of print) Lonely Planet's Hiking in Japan. Lonely Planet's guides range from good to awful, but this one was a good pick.


I went to Kyushu last August (and the weather was quite nice and not hot, thank you). Here's my thoughts:

• Nagasaki was very nice, and great for walking around. However, I think we literally went just overnight - it's not a big city, and you can really see all the big sights all in one day/night. It's beautiful, though, and the atomic bomb "areas" are haunting - and I think it's a better memorial area than was Hiroshima, but that's because it seems to be less "tourist-y", almost. But once you've gone to the museum, to the "eyeglass bridge," had your bowl of Nagasaki champon, and ridden the gondola to the top of the mountain...it's pretty much over - I'd say it's the equivalent of a cruise-stop in the Caribbean for most people (and it is a cruise-stop for several lines, actually).
• Fukuoka (Hakata) is pretty great. It's not "pretty" like Nagasaki, but if you like eating, the nighttime food stalls (yattai) may make it the greatest place in Japan. It's a bigger city - with a greater "international" flair than Nagasaki, so it's got a better population for going out and just meeting people, if that's your thing. It's also famous for Hakata Ramen, which is delicious. There's a number of interesting temples, and it's fairly close to the old shrine/temple city of Dazaifu. It's also the closest place to Korea, and I am fairly sure it's from where the high-speed ferry to Busan leaves.
• Beppu, on the other side of Kyushu, is famous for hot springs. I didn't go there (but mainly because it was August, and I went to the beach instead, heh). If you're looking to relax in Kyushu, it's probably the place to go. You can also visit the "hell springs" there, which are not for bathing - they're for looking at.

I don't know enough about Shikoku, but I've heard that Kochi is supposed to be beautiful. And if you really want to go off the beaten path - and you're REALLY HARDCORE - you can hike or bike (or yes, take a bus) the 993 mile Shikoku Pilgrimage.