Tokyo has become a photographic cliche. Ex-english teaching blogtaerds have beat you to the punch. Get into the sticks. Buy Hexars and 67s and Voigtlanders and...Forget Yodobashi and Map.
Good luck finding film for sale, or getting it processed out in the sticks. Few of the old mom-and-pop camera stores exist anymore, and those who do will only do digital prints on the spot, film will be sent to a lab in a larger city.
I love the countryside in Japan, and I spent my first year here living in a small town quite far from a major city. If you like old temples, shrines, farms, and traditional architecture, you should spend a little time in the countryside. The big cities have more to offer in modern architecture, "interesting" (bizarre) people, and shopping.
I live in an apartment a few minute's walk from Tokyo station, and my office is near Asakusa. I usually walk from one to the other, and I almost never fail to find something interestng enough to photograph during my commute.
The time of year is important when choosing what areas to visit. In the winter, the cities are the best choice. The weather is somewhat cold in Japan, and it is nice to e able to duck into a shop or store for some coffee or tea. In the spring or fall, the countryside is the most colorful. Cherry blossom season arrives in Tokyo during the first week of April, this is generally the best time to visit. The forests around Nikko are beautiful in the fall, but I prefer the foothills around Kyoto. The best time to go is around the third week of November. The timing varies + or - one week, depending on how warm/cool the year has been.
Summer is festival season; each city, town, district, has it's own festival, and these are often noisy, fun, and colorful. There is music, food, and decorations, as well as dancing and contests. The food booths and souvenir stands are often attended by junior gansters (yakuza), who are interesting to photograph. Foreigners can get away with a lot in Japan, even taking pictures of yaks.
City life is quite interesting. The young women in maid costumes in Akihabara, the young "hosts" hustling potential female clients in Kabukicho, the often unshaven ladyboys strolling around Shibuya or east Shinjuku, there are endless things and opportunities to photograph.
I'm sure you'll have a great deal of fun,