David,
We went for 2 weeks in October, 2013. We're a couple in our 60s who have traveled Europe, etc. Same requests as you, Rick Steve's travel experiences. Here are my recommendations. Buy a Japan Rail Pass. It will cost you about $500 each, for two weeks. Plan on validating it so that it will cover your last train trip to the airport. If your trip is 15 days, you can manage without the pass on the first day in Tokyo by walking around the local area or using the subway. In Tokyo, stay in Ueno area. It is easy to access from airport (Narita) and it is convenient for trains. Ueno is also jam packed with museums, art, history and authentic neighborhoods. Some areas are very old and still inhabited by families (not just young people.) Locate the local guide for this area at Ueno Green Salon (in the Ueno Park.) There is a free 90-minute walking tour of Ueno that departs from here every Wednesday, Friday, and Sunday at 10:30am and 1:30pm. All you need to do is show up. It was one of the highlights of our trip. We were shown the historic Ueno, temples, shrines and other buildings. Our guide was charming and spoke excellent English. It actually took about 2 hours. These tours are also available in other cities and areas of Tokyo. From Ueno you can easily get to all areas of Tokyo on the Yamanote train line. We stayed in two places, and I would recommend both: Hotel Coco Grand Ueno Shinobazu-large hotel with friendly staff and fantastic Japanese and Western breakfasts included. Nice first hotel to get acclimated. This is not an inexpensive hotel ($140) but reasonable for Tokyo, and it is close to restaurants in a busy area. A totally different experience was the Ryokan Sawanoya Ueno. It is a family run ryokan located in the authentic "old" part of Ueno and very Rick Steve's feeling. It would be in his book, if he had one. Very helpful, modest, clean and quiet. From Tokyo we spent 2 nights in Kanazawa. Ryokan Sumiyoshiya is a lovely but not very expensive place to experience a traditional ryokan. Indulge in a dinner served in your room. This is a great city for historic neighborhoods (it was not bombed), crafts, and one the most beautiful gardens anywhere. Because of the autumn celebration in Takayama, we spent 2 nights there. It is a bit remote to get to, but a pretty mountain town. Then 5 nights in Kyoto, and I cannot recommend highly enough the hotel Eco+Tec. It is the perfect Rick Steve's match in Japan. It is located in a prime Kyoto neighborhood, quiet street, but close to transportation and sites. It is very reasonably priced, clean, and has helpful staff. We loved Japan. The historic sites are so beautiful it takes your breath away. The Japanese people are polite and helpful, food is sometimes difficult to locate (lots of signage is only in Japanese), it got dark pretty early, transportation was easier than it looked online, making reservations for hotels online worked out, but the sites are often difficult to understand-room size, etc., and train passes made travel extremely easy and pleasant.
Molly