Depends what you are interested in.
If you like temples and shrines then clearly you are in the right country.
Matsushima Jinja was very interesting. Quite out of the way. Nice scenery. The only way to stay on the island was inside the shrine in one of the rooms they kept as a Youth Hostel. Don't know if they still do that. Highly recommend it.
http://www.matsushima-kanko.com/en/index.html
The shrines and temples at Nikko, north of Tokyo, are very colorful and interesting. Probably worth a couple of days stay. One day is OK but you'll feel rushed.
Sanjusangendo near Kyoto station is kind of amazing (Google image) but you can't take photographs on your own inside.
Miyajima is a nice place to visit. You've probably seen photos of the large torii in the water. There is an extensive shrine all built over the water. Lots of interesting things to photograph.
Heian Jinja in Kyoto was interesting. The shrine is totally painted in a vermillion color and there is an extensive garden.
I liked some of the scenery. The lighting is usually soft due to the humidity. There is often a lot haze.
I found a lot of ordinary life interesting; coffee shops, vending machines, architecture, railroads. The Tsukiji fish market is fun. Akihabara is great for night photography. Probably more neon signs here than anywhere in Japan.
A lot of what I found interesting in Japan is hard to describe. It was opportunistic. Not worth a trip as a destination, but you just go walking and keep turning on smaller and smaller roads till you find some too small for cars and there will be some really charming noren hanging outside a restaurant. Those things are where you find them.
For a change of pace you can visit China town near Yokohama. Just up the hill is the area where the foreigners were first allowed to live. There are some lovely international schools. My kids attended St. Maur's part of the time when we lived there. There is an old cemetery you can find with graves hundreds of years old.
For macrophotography you can find all sorts of interesting little objects to photograph. Go to any stationery store, or gift store or electronics store and you can find all sorts of little things that people hand on their phones or their bookbags and such. I recall that KFC in Japan for a while gave away little plastic dolls of the Colonel that were made to hang on to the straw in your softdrink. This stuff is everywhere.
In Ginza there are a couple of places that sell beautiful washi, Japanese paper. There was one at the main Ginza crossing across from Wako department store. It was a small place just off the corner. Itoya in Ginza also sold this paper. You have to ask because it was at a small place not far from the big Itoya building. These are quite lovely as backdrops for pictures of other things. Usually you are not allowed to photograph inside the store.
Any drinking and eating area of any city is interesting in the evening. If you catch it just at dusk there is a nice balance of natural and electric light.
Once in a while in the evening you'll happen upon a line of at least two hundred taxis. Or a bike rack with five hundred bicycles.
Don't know if they'll let you photograph it but I recall once visiting the lost and found in Tokyo station where they kept the lost umbrellas. There must have been ten million umbrellas.
Have fun. Where are you going? Sophia University?
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