Thanks for the update. I get a better idea of what you are looking for.
Without being nosy I would like to know if you have travelled to places where most people DO NOT speak English.
This is one of the major problems in Japan.
In lower cost hotels mostly but even in international ones, the staff will know enough English for checking you in-out, tell you about breakfast, keeping your suitcases, but it is very very basic.
Once I was lost in a wealthy looking residential area of Kyoto when a lady came out of a home and was about to go in another one across the street when she noticed me. With my few words in Japanese, her few words in French (my 2nd language) and English (my 3rd),we managed but it was slow going..
I have talked to a few university students and they were painfully slow in English, and marginally better in French.
You might try to ask a major tourist bureau in Tokyo etc. about volunteers guides (Goodwill guides). At least you would have someone to talk to..
http://www.jnto.go.jp/eng/arrange/travel/guide/guideservice.htmlAbout homes for rent:
http://www.japan-experience.com/rent-a-house-in-japan?ap=j0095gThey are short-term rental specifically for foreign tourists.
Apartment-hotels:
http://www.tokyustay.co.jp/e/ Don't hope too much about Tokyo. It only became the capital in the late 19th century and was badly destroyed by an earthquake in 1923, rebuilt quickly and cheaply, then bombed into nearly total destruction during WWII. There are a few old unscathed districts, with old wood houses and temples, and also some great modern buildings, but most of Tokyo is an architectural wasteland. Though it does have great parks and gardens.
At the same time it is extremely vibrant, frantic and all that.
The Kansai, on the other hand, is the true cradle of Japanese civilization. Osaka was-- briefly--the first permanent capital, replaced by Nara, then finally by Kyoto.
Kyoto was spared by WWII bombs and was a capital for 1000 years. It has thousands f temples and shrines
There are about 22 million people in the Kansai...
The areas with colourful, alternative and eclectic lifestyles I am familiar in hometown in Canada but also in Paris and other towns I know are not near universities, not that you wanted both necessarily together.
At rates, be prepared not to hear much English at all, besides other tourists.
Japan has a lot in common with Europe (the great transportation--overcrowded and all--the huge number of bikes all over the place, compact houses with a sliver of a garden on narrow streets (streets that don't even have names) but is also very very different.
Expect to be on rather unfamiliar grounds. expect to be in a crowed public place and not hear a single familiar word, only the background music made by Japanese talking to one another.
My best buddy (born in Japan) and I favour economical business hotels, unless we can finagle a luxury room in a high class hotel for the price of the lowest single..
http://www.toyoko-inn.com/eng/This one is bit more expensive but cheaper enough if you book in advance (we like to wing it):
http://japanhotel.net/Are you aware of the economical JR pass (good for travelling long distance cheaply)?
http://www.japanrailpass.net/ JR is divided in 6 rail companies working as one. Tokyo is under JR East, the Kansai under JR West but the pass is good for all the 6 companies (the pass must be bought outside Japan, in your country).
For fares on various trains check
http://www.hyperdia.com/en/ (you need to remove shinkansen trains if travelling on regular trains,and vice versa.
I have travelled to Japan on my own a couple of times, hardly talking to anyone, and found it very relaxing (at the time I had to interact with about 150 people at work, day in/out).
I hope that you will be willing to go out of your comfort zone and discover Japan..