I've never heard this. What is your definition of a nice hotel?
If you only want to stay at SPG, HH, IC, and Hyatt properties, then you'll find that most of your options are in the largest cities. But just about any city will have at least one up-market Western style hotel - albeit without the opportunity to earn points that you can use back home. If you expand your criteria to include traditional Japanese inns, you'll find very comfortable lodgings in every corner of the country.

Yes, except substitute "Kyoto" for "Osaka" and "train" for "shinkansen."

While the shinkansen (bullet train) may indeed be the best option for day trips, local or deluxe trains may work better at times. From Kyoto (or Osaka for that matter) to Nara, there is no shinkansen but the local trains provide fast, frequent connection to the ancient capitol.

If you are on a JR Rail Pass, you can use either shinkansen or local JR trains as needed.

I'm surprised that you think "hub + shink" tourism is better than staying in smaller places abmj. Is that really what you mean? I know that you've wandered far off the beaten track without feeling the need to rush back to the big city on the last express train before nightfall.

That's what we are looking for. The wording "nice hotels" was indeed wrong.
How can these Japanese Inns be found ?

Guidebooks to Japan often list inns in various regions. As for online resources, you'll find a number of sites mentioned on the forum threads. Some of the sites that I can think of include:

http://www.ikyu.com/en/
http://www.ryokan.or.jp/index_en.html
http://www.japaneseguesthouses.com/index.htm
http://travel.rakuten.co.jp/en/
http://www.japanican.com/index.aspx

You can find some commentary about the various sites on this page:
http://www.jnto.go.jp/eng/arrange/ac...ons/links.html

You are correct that I tend to wind up in little business hotels in places like Matsue or Kochi. I was thrown off by the poster's reference to "nice" hotels like SPG or IC and the desire for similar places in smaller cities. If one wants an IC, I stand by my advice. I see, however, that the poster has clarified and such accommodations are not really necessary. In that case, I am with you. On my last long stay, I actually stayed a few nights in Nara instead of Kyoto or Osaka as well as several other other somewhat out-of-the-way places. Not a single night in Tokyo, Kyoto or Osaka. :p

If the poster is ok with smaller, local hotels, then I think the "hub-and-shink" method (love that by the way) is not the most efficient or enjoyable way to see Japan.

It all depends on what you like.

Personally, I hate packing and unpacking. If I base myself in a central city, like Tokyo or Kyoto, the marvelous Japanese train network ensures that there's more to see within day trip distance than I can possibly cover in one trip.

For example, during one stay in Tokyo, I made easy day trips to Nagano, Mito, Aizu-Wakamatsu, and a client in Fuji-shi, and spent a night with some Japanese friends who have retired to the Nasu area.

From Kyoto, I've ventured to Nara, Osaka, and Kobe (of course) but also to the burial mound area, Yoshino, Tenri, Uji, Muryoji, and Hikone.

On the other hand, sometimes rural peace and quiet is what you need. I once spent a night in Ohara just for the atmosphere, even though the village is on the Kyoto city bus line. For Koya-san, a night in a temple is an integral part of the experience. In other cases, such as when traveling in more remote areas, you have to move from place to place.

Excellent; thank you ^

To the OP on the question of your extra day, I would use it do something else in the Kansai area. Kyoto is pretty central. So you could do Nara, Osaka, Kobe, or go to Arima (an onsen town near Kobe).

As others have said, Japan is really not that hard to get around in for a non-Japanese speaker. Also, in the last decade the use of English or at least Romaji (Romanized Letters for Japanese words) have increased a good deal in signage so it is even easier than it used to be. Enjoy your trip to Japan.

It's better to use Tokyo and Kyoto as hubs, not Osaka.

Nara can be done in an easy day trip from Kyoto (also from Osaka).

Nikko is a bit further away from Tokyo but can still be done as a day trip. There are no chain hotels in the Nikko area AFAIK, but virtually all Japanese hotels are clean and safe, so you don't need a chain hotel. A night in a ryokan or onsen would go well with a visit to Nikko.

I know there is that saying about Nikko that all the guidebooks will translate for you, but after you've seen Kyoto and Nara, I am not so sure you really need to visit Nikko.

July will be hot and humid. The early part of July can be part of the rainy season.

I did get my rail pass exchange voucher. How essential are seat reservations, particularly for the Tokyo-Kyoto train (to on the 16th, returning on the 20th, mid-day both times)? If I do go for a non-reserved car, how do I tell which are reserved cars and which aren't?

Reservations aren't essential, but they're very easy to arrange and they cost nothing if you have a JR pass. I'd certainly recommend making reservations for any long journey that you take.

If you're using a JR pass to ride a train without a reservation and you find that the unreserved car is full, conductors should let you take an available seat in an unreserved car. However, it's best to wait until the train has left the station to attempt this. If you take an unoccupied seat in a reserved car when the train is at a station, there's a good chance that someone will show up with a reservation for that seat. Alternatively, the conductor may warn you that you're going to have to vacate the seat at the next station because someone reserved it from there.

For Shinkansen trains, information about which cars are reserved / unreserved / green is shown on the electronic displays above the platform. There are also signs at the entrances to every car that indicate reserved / non-reserved.

There are also labels on platforms (and hanging on wires above platforms) that indicate the type of car at each point on the platform. However, these can be very tricky to interpret, because many different train configurations use the same platform and you need to know which labels are associated with the train that you're about to catch.

I disagree and think that Osaka is a better hub than Kyoto; but it really depends on how long you're going to be there and what you plan to do.

Why do you feel that way?

The reserved and unreserved cars are marked in both Japanese and English, so there shouldn't be any problem.

Trains leave Tokyo for Kyoto every few minutes, starting at 6:00AM. As long as you're not in a peak travel period, reservations should be no problem. But it costs nothing to make a reservation, so just go to the reservation office in Tokyo station and tell them about what time you want to travel. (Write it down if they don't understand.)

I prefer Kyoto as a hub because you're closer to the major sights, there's plenty to do in the evenings unless you're a hardcore partyer, and it's just a more pleasant environment all around. (Osaka is even more of a concrete jungle than Tokyo.) Also, you have only one train station to deal with for day trips, as opposed to three (Shin-Osaka, Osaka-Umeda, and Nankai Namba).