Hi jkid-san (I'll resist -kun although your username would suggest it
I haven't been to Tokyo.
It's a modern high-rise international style city mostly.
There are small "historic" parts hidden away, and the Castle park is nice (although the castle is a concrete reproduction) and there is a major bunraku (puppet) theatre but it might not be what you're looking for.
(IMHO and not wanting to offend anyone. A lot of Japanese cities were destroyed in WW2 / Pacific War. The buildings were mostly wooden and firebombs were used. The figures I've seen cite 90% plus destruction rates. Mind you Earthquakes had had the same destruction at times but in postwar reconstruction they took to concrete and international style in a big way and I'm not sure they have a concept of town planning at times.)
I probably should have explored Osaka a bit more but the craziness of nipponbashi district got to me and I headed elsewhere.
What you might be looking for is in Kyoto, Nara, Koyasan, Ise, Himeji. All in the kansai region that was for a lot of Japan's history the seat of power.
Kyoto is the big one (unbombed -- but I've read that it was an alternative A-bomb target because of this)
I found it to be a bit more human in scale and had the sort of things I wanted to see. OK it's sort of like people looking for leprechauns in Ireland or Beefeaters, Bobbys and Castles in England but that's tourism for you.
So Geisha are the big symbol of Kyoto. But I found that you see them, glimpse them by accident, in the back lanes of Gion not by staking out the expensive restaurants like the tourists with cameras.
It has an abundance of World Heritage sites including famous places like the Golden Temple and the Zen Rock Garden at Ryoanji. The important thing to figure out is most of the temples are on the hills surrounding Kyoto and not in the center. (There are some big exceptions to this) As a European I found this town plan style hard to figure out with my ideas of town centres growing up around a forum or church.
Nara is smaller and quieter but has a fair amount of buildings to visit in a park on the edge of town.
Ise has an important shrine (although a lot is off limits). There are archaeological sites but I found these visually disappointing. The Japanese built from wood. It doesn't last so an archaeological site often consists of postholes. The wood thing also has another interesting facet of renewal -- the buildings are constantly being rebuilt. Indeed this is a religious ritual at the Ise shrines.
There is also a sort of reproduction district by the Grand shrine while not historical as such it has a nice feel to it.
Himeji has a great castle. (It was used as a location in the TV series Shogun)
Koyasan is a Buddhist settlement high up a mountain. Well worth staying overnight at a temple here. A small town full of temples and an important cemetery.
Osaka, Kyoto, Nara and Himeji are all close together. I would base myself in Kyoto and have day trips to Osaka, Nara and Himeji. You probably should experience Osaka by night as well but for a historical feel Kyoto is the place to be.
Ise and Koyasan are a bit more off the beaten track and perhaps a bit more effort to get to, but Japan's railroads must be the best in the world so it can be done.
Check out the travel to Japan threads here
Read some guide books. Check out Google Earth.
You can get too much of temples at times and it's worth exploring the other things Japan has to offer. Onsen! The neon nightlife craziness. Karaoke.