I went to Japan in May 2009...
I am not a big fan of big tour groups, so I was excited to find Esprit Travel
http://www.esprittravel.com/independentjapan/local.html
We told the travel agent what we wanted to see...she also had a variety of suggestions. We were given an itnerary to follow (if we chose to). They arranged all of our trains and hotels. We had a personal tour guide for 1 day in Tokyo, and a personal tour guide for 1 day in Kyoto. It was the perfect trip. No pressure to follow the herd...
The tour guides gave us opportunities that other travel agents didn't offer. I know this from talking to people we met at dinners and bars. Everyone wanted to know the name of the travel agent we used. For example, in Tokyo, we had the usual sightseeing of the Fish Market and temples. But, our guide arranged for us to have a blessing at a Shinto Shrine. It was VERY cool. In Kyoto, we spend a few hours with a calligraphy master in his home/studio. We also had a private tea ceremony with the abbot of a Zen Buddhist monastery.
Basically, they will build the trip you want. You just tell them what you are interested in doing.