Bloodstone003,
Just returned from 2 months there.
The JapanRail Pass is a fantastic deal IF you are planning on traveling long distances a bunch. To see if the "payback" is there, go to the Hyperdia site and load in a few of the travel plans you have. (
Enter the station name ) The fares for those trips will show. Compare the costs to the cost of the Railpass. Then you can decide if a one week, two week, or three week one makes sense for you.
The above comment about "spending your life on trains" is a VERY true one. The shinkansen trains themselves are certainly VERY fast....... but there is a lot of time used in getting from station to station, platform to platform, and waiting for the trains themselves to assure connections. Local trains have even more of this factor because they themselves are slower. Planning in advance helps a lot with this factor to be efficient in the use of travel time.
One place that is not too far from Tokyo that is pretty amazing...and has a LOT to see in the "hiking" category......, is Nikko, in Tochigi-ken. The shrines and temples there classify as a "World Heritige Site". The mountainous landscape is beautiful. There are tons of trails. Don't miss walking along the river thru the gorge with the Jizo statues (it is on the local "tourist" maps) to the southwest side of town. The downside is that Nikko is a MAJOR tourist attraction and close to Tokyo, so it can get crowded at times. Go on a rainy period...... it is still beautiful...and the crowds disappear.
Check out the Chichibu area to the southwest of Tokyo. A lot of history there, and still some what is left of the "old" Japan has its last vestiges there.
Try to get to a real onsen at least once. It is a VERY "Japanese" experience. There are many all over Japan, thanks to the volcanic nature of the islands. Day visits are generally actually rather cheap; it is more expensive to stay at one.... but not absurdly at most.
If you are an "adventurous eater", try to eat at little "hole in the wall" places that the locals use. If you don't have the language skills, it might be a bnit "interesting" sometimes to get your food...... but generally the food will be fantastic. And WAY cheaper than at more "tourist" oriented places. And more truly "Japanese".
Also, take a couple of friends and hit small izakaya (little bar/eating establishments that seat maybe 10 to 20 people) in the evening for Nihonshu (sake) or bieru (beer) and some FANTASTIC bar food. Another truly "Japanese" experience.
Head for the prefectures and cities that the tourist brochures DON'T tend to list. Harder to plan and schedule, but you'll see more of the "real" Japan.
Gotta' go.
best,
..............john