My husband and I spent the last three weeks of June in Japan and found the experience even better than we had anticipated. We spent 3+days in Tokyo, 4-1/2 days in Kyoto, an overnight in a Buddhist temple on Mt. Koya, 3 days on the western coast of Honshu in Tsuwano and Matsue, a stopover in Nagoya, then 5 days in the Japan Alps (Matsumoto, hiking in Kamikochi, and staying in Takayama), returning to Tokyo.
Trains: We liked having a JR rail pass for the whole 21 days and found rail travel delightful. For instance, in Kyoto, when we decided to walk up to Fushimi Inari (highly recommend), we just showed our rail pass at the window and went a couple of stops out of town. Train cars had a digital display in both Japanese and English announcing the stops, as well as an audio announcement. We mostly made seat reservations a day or two in advance (no cost), just for our own comfort level, but found it easy to change them when the situation arose. We found it easy taking the Narita Express (after exchanging our voucher purchased in the U.S. for the actual rail passes at the Narita JR office) to Tokyo station, and on to our hotel via subway, getting a Pasmo for the subway first in a pink Pasmo machine in the bank of machines in the metro. Since the rail pass excludes Nozomi bullet trains (the Hikari it does include are just about as fast), reserving ahead helps to get the connection worked out for a longer trip. If you do travel by train, you will thank yourself if you have just one carry-on size suitcase. Although most stations have escalators, at smaller ones, you have to walk up a flight of stairs, over a pass, then down another flight to get to a particular platform. Also, some subway entrances don't have escalators. Having been followers of Rick Steves for Europe for years with quick-drying and low-wrinkle clothes, we have found that we can fit all we need in one carryon bag, with the before-dinner daily ritual of washing out a few clothing items. (We brought a stretch line and 8 plastic clips, and were surprised to find a number of nice hotels had a stretch cord beside the shower rod.) The city stations had a Vie de France bakery--really good sandwiches and salads for take-away (not to mention the best double chocolate croissants you'll ever taste).
Dress: Japan is conservative, and people dress nicely. Even in the warm weather, women wore short-sleeve, rather than sleeveless tops (definitely no tank tops), and they wore leg covering (either flesh-colored stockings or those thin nylon leggings with a bit of lace at the bottom if the skirt was shorter than calf length. Many wore capri pants. The whole three weeks, we saw maybe 3 men wearing shorts.
Hotels: We liked all of our hotels, which mostly were conveniently close to train stations. The ANA hotel in Kyoto was not only a great rate for the 4-star level, free internet, conveniently located right on top of Nijo Castle and near bus stops to sights, but has a free shuttle to and from Kyoto Station (which we used not only for arriving an departing, but sometimes for our daily sightseeing when we would start or end up at or near the station), so it saved some money and hassle. The only drawback is that their restaurants are high end except the cafe. Our experience staying at the Buddhist monastery ryokan Shojoshi-in on Mt. Koya was especially memorable (booked through Japaneseguesthouses.com). The ryokan-style Tsuwano Lodge is a bit of a walk outside of town center, but very friendly and great food. In Matsue and Matsumoto, the standard Tokyu Inns were so conveniently located near train and bus stations. For Kamikochi hiking, we really liked staying just outside in Hirayu Onsen at the hot spring spa Hirayu-no-mori (lovely indoor/outdoor baths, excelelnt food, and reasonable). In Takayama, we opted for comfortable beds at the Best Western (good Visa rate on internet) and enjoyed the fabulous complementary breakfast buffet. The Hotel Monterey Akasaka in Tokyo was very nice--comfortable bed in small room, good and reasonable French restaurant, quiet location in government district, lots of tiny Japanese restaurants in nearby Mitsuke, Starbucks and Kinkos (for internet use) just down the street, and easy 3 minute walk to Akasaka-Mitsuke subway for easy connections all over.
Kyoto: The TI on the 9th floor (access from elevator inside the department store in the Kyoto station) is so helpful! They have leaflets on suggested walking tours and a person who speaks impeccable English. If you are going to Mt. Koya from Kyoto, by all means go over the practical logistics with them (we ended up purchasing a Free Subic pass for Mt. Koya and found it convenient. It takes over for the private r.r., cable car and buses after the first leg on the JR line with the pass). Also, in the Cube on the 11th floor are several Japanese restaurants (signs in Japanese)--we liked Togata. For the famed Ryoan-ji temple, if you want the meditative experience at the dry garden, I suggest going very early, or we found that the crowds thinned way down at noon for lunch. In addition to the big-name temples, we really liked the garden at Tenryu temple in Arashiyama (a local train ride). You can also walk further in the area, e.g. through a bamboo forest.
If you like woodblock prints, the museum in Matsumoto is great. Access takes about 1/2 hour: a few stops on the local train, then walking (directions posted on wall of train station shed), or a short car ride.
There's a beautiful new, modern art museum in the city of Matsue--right on the water and in a lovely park, known for sunset-watching (also has a very good Italian restaurant). Matsue Castle is also very good with exhibits (we liked it better than Himeji, which we could have skipped had we seen Matsue first). Tsuwano (in a beautiful valley) and Matsue (nice small city on water, well marked for sights) are little-visited by Westerners (I can't remember seeing any other non-Japanese in our 3 days on the Western Honshu coast), very friendly places, good food, etc. The train ride up the San-in coast betwen Tsuwano and Matsu on a Hikari train is pretty, too.
The Hida region TI in Takayama also has a person fluent in English. I found it very helpful emailing her back and forth in the months before the trip to work out some logistics, and she reserved Hirayu-no-mori and a day bus trip for us.
If you're reading this and about to visit Japan, I hope that your experience is as enjoyable as ours was. My husband, who has a Master's degree in Japanese and Chinese history, says being in Japan reminded him why he was so interested in studying this culture and history in the first place (and he can't stop marveling at how spotless all the cities in Japan are). I hope some of these tips help, as I was helped by those I read.

Great report, thanks! Any photos?

Thanks for the report! Sounds like you had fun.

Congrats on finding the pink pasmo machines on your first trip to Japan....although three weeks is a long journey. It took me till my third trip to Japan to finally realize why there were these pink colored machines next to all the other ones....., lol

I had forgotten about the Cube in Kyoto Station. I love that station and all the shopping and food venues inside. I don't think it gets mentioned enough on this forum on just how big it is.

Glad you got to get out into the countryside for a few days. Life is very different in rural Japan compared to the city life.

Planning a return?

Aloha!

Always good to put prices/costs in your report for hotels, restaurants, transportation, etc- it gives people a better idea of what things will cost- especially in Japan where costs tend to be much higher than in other parts of Asia.

I am glad it was even better than you had hoped!

Thanks teacherhiker - we will be in Japan in three weeks. There will then be a fourth person wearing shorts - I can't stand the thought of long pants of any type in hot humid weather.

Thanks so much! Reading your post was so helpful to read in planning our trip to Japan

Thanks for the report. It sounds like you had a wonderful trip. I would love to know the email address you were using for the Tourist Office at Takayama.

Let me add my thanks to the above. We are leaving tomorrow for Japan and Bali so appreciate all the help we can get.

Great report! We spent the first 2 weeks of June in Japan and also enjoyed it much more than anticipated. So much so that we are already planning to go again next June. This time we will skip Tokyo to add much more time to Kyoto and Hakone. We had read a lot about the Station and the surrounding area, and are so glad we booked the Granvia. What a great city Kyoto is. With all the positive things I'm reading here, I'm trying to think of a negative to warn people about. I'll keep thinking.

Nice report! How did you like Takayama? Did you see/do much there? The BW there was a really good choice. What was the bus day trip that the TIC person arranged?

Matsue is a nice place to visit. Your comparison of Matsue castle with Himeji is interesting. Did you also visit Matsumoto castle and how does it compare? Did you visit Izumo? No Hikari on the San-in line (more likely was an Oki or Matsukaze limited express).

You mentioned spotless cities. Yes. In Matsue, though, I noticed a bit of trash, cig butts. Nothing like in other countries, but different from elsewhere in Japan. I wonder if you noticed.

RE Takayama: I seem to have deleted my email correspondence with the Hida TI office, but I found this: [email protected]. Hope that works. Would recommend the Takayama jinya (preserved govt. house--the TI can get you into an English langauge tour a few hours ahead), Hida Folk Village, and walking the streets with preserved Edo-period shops (could be 1 day total). We decided against the day in Shirakawa-go, for which the Hida TI will book the bus by email, because by the time we arrived in Takayama, we had seen enough of preserved rural villages in other places. (takes most of a day).

Thanks for that. I have sent an email off. Hopefully they can fix up some bus reservations for me.

Bookmarking to read later.