I have been to japan.. and taking a single 50mm would be a mistake. There are many temples that do not allow flash or tripods. in those cases a VR lens is invaluable. They are also quite small and with amazing nooks and crannies, so a wide angle lens is essential.
I had my 18-70, 12-24, 18-200vr and Sigma 150 macro. I found the nice little 18-70 quite adequate but the 18-200 was most used mainly due to the convenience and the VR, but it was not wide enough in the temples, the 12-24 was not able to get pictures bec of the low light, but for sceneries it was great.. I am not really a fan of the wideangle ranges though that 12-24 is a really nice lense. I like tele shots but bec japan is so closed in I didnt use the 200 end much. The macro lens was great, lots of tiny things and trinkets to shoot :-). If I were to do it again and had only one lens I would take a 16-85 VR(Plus my DCR250 for macro), and an AW-100 for when it rains and snows or when I go skiing( LOL skiing with a DSLR was not the most fun thing!, but I did get some nice pics !). I would probably take a new 70-200 F4 too :-) .. cant live without my tele end ! :-)