Here's some info from my last trip-
Tokyo- what you'd expect. Capsule hotels are good if you're alone & trying to budget. They're clean & loaded with floor after floor of facilities (restaurant, chillout room, massage, bathhouse etc etc) & only about $40US per night.
Kawaguchiko- Near Fuji. Beautiful little resort town, old Japanese feel, big lake that's great to ride a bike around. Also near the Suicide Forest from the well known VICE doco.
Fukuoka- Nothing special but probably the easiest girls I found in Japan if you wanna be a manwhore, not really my thing but the complementary suntory whisky @ the capsule I stayed in def weakened me. Lots of Koreans & Taiwanese.
Kyoto- Only here briefly, but I remember there being lots of temples/alleyways to explore from my first visit.
Hiroshima- the memorial @ ground zero is very dignified, I didn't get much further than that.
Yakushima- This is like the garden of eden & was my highlight for sure, but you need to hire a car, or ideally a motorbike to get the most out of it.
