When you program your trip in Japan, keep in mind the rainy season. You won't loose much by avoiding it, because most of the important events or festivals in Japan are also scheduled to avoid the rain. And if you like taking photos in the rain (as I do), you'll have lots of chances anyway, because there are quite a few precipitations during spring, summer and fall too, sometimes even torrential rainfalls, like when I took this photo in the Kichijoji Station from Tokyo...
EXIF info:
Nikon D90
Lens: VR 18-55mm F/3.5-5.6G
Focal Length: 18mm
Aperture: F/5.6
Shutter Speed: 1/30s
ISO Sensitivity: ISO 400