I travel to Japan regularly but wouldn't go there for a holiday, they have a great line in urban sprawl (take the 3-4 hour shinkansen (bullet train) ride from Tokyo to Osaka and you won't see anything but buildings out of the window), it's also massively overcrowded in the cities.
This doesn't mean that there aren't nice bits, I'd recommend a trip to the top of Mount Azo on Kyushu island and have seen some great temples in the countryside around Yokohama. One of the major disappointments is the Japanese Castles, they're all billed as being incredibly old but if you ask around they were all rebuilt fairly recently (Nagoya Castle was originally built in the 14th Century but rebuilt in the 1960's), the Japanese don't seem to think that rebuilding something affect its history.