1

Tokyo itself will fill several days. There are several good day trips around Tokyo including:

• • Hakone (buy the Hakone free pass (Google it) and you can see the whole area, which may be lovely in early October) That could easily be made into a 2-day trip.
  • Yokohama and Kamakura
  • Nikko, but it is a bit further away and therefore more expensive to get too. The natural scenery may be lovely at that time of year though. (The temples are under restoration.)

2

The Japanese Alps fill most of the conditions if you stay in Matsumoto a day or two and then go into the mountains for a few days.
or Nagano and the surroundings.

3

I'd consider Tokyo with day trips.

Tokyo itself is not all hypermodern neon lights, but could well fit some of your requirements: visit a traditional garden or two, stroll through Yanaka, see Meiji Shrine and Sensoji and some more obscure temples such as bound jizo, Zojoji, Sengakuji,... see a traditional theater performance (kabuki, noh, bunraku,...)

Take daytrips to Kamakura (temples and green hills fine for a walk), Hakone (various sites and nature). Do an overnight (two day) trip to Nikko seeing the sites around Nikko and go hiking in Nikko NP (e.g. Senjogahara) on day 2. You can end the hike at Yumoto Onsen. Explore some less popular places around Tokyo such as Kawagoe, Nokogiriyama,...

4

thanks so much for your suggestions....domo!

5

I'd go with Japan Alps as well...as above,a week around Matsumoto and Nagano areas with lots of countryside stuff available too.

6

I would recommend the Japan Alps, but based on settling yourself in Takayama. Daytrips to Kamikochi, Shirakawago (overnight would be even better), Hida Furukawa. Then finally stop by Matsumoto for the castle before returning to Tokyo for the flight out.

7

I live in Saitama city, and I can tell you it's definitely a good place to stay with many historical sites. If you like mountainside, I recommend Nagano. If you like seaside, then Shizuoka cannot be missed! 

8

I lived in Tokyo a few years back and had Japanese friends who took me to some lesser known tourist sights around Tokyo - some of these places you can't even find in the Lonely Planet guide and are more popular amongst the Japanese than foreign tourists. None of them are what I'd call amazing, but they're pleasant enough to visit and are great for getting away from the crowds found at the most popular sights.

Shibamata, only 15mins east of the Yamanote line, is a great day trip. It's basically just a street lined with old wooden sweets and souvenir shops with an interesting old temple at the end. The temple is notable for an ancient pine tree in its grounds - the branches ar so long they need wooden supports - and some amazing wooden carvings on the walls of the temple itself.

There are some great walks in the mountains near the western end of the Chuo line. Mt Takao and Mt Mitake were the two that I recall doing, and both were easily accessible by train (40-60mns or so each way). Mt Mitake had a funicular car travelling to the peak which which had a few temples, shops and restaurants, while you can get great views of Fuji from Mt Takao if the haze isn't too thick.

Enoshima is an island off the coast southwest of Tokyo (not far from Kamakura). There's a causeway for easy access from the mainland and escalators around the island if you're a little leg-weary (this is Japan after all). It has the usual temples, restaurants and souvenir shops that you can find at any Japanese tourist spot, and you can also see Mt Fuji looming impressively over the coast on a clear day. The island gets really busy on weekends.

Finally, Kawagoe is another town on Tokyo's outskirts with some impressive old shops and other historic buildings. There's not much to it - a couple of streets at most, but it's a pleasant enough diversion.