Where to Vacation from your Vacation in Japan?

How about an Ohnsen in the Hakone area?

I did think about Hakone, but felt a little deterred early on by reading about the crowds. I was a little trepidatious about heading there after the crowds of Tokyo, especially since we'd be headed there on a Saturday. I thought Nakasendo might be little more off the path (though I recognize probably still busy). Do you recommend Hakone in particular?

Nikko is a cute little town with lots to see and nice restaurants. It is busy with tourists during the day, but quieter at night. We really enjoyed it and it's small and manageable. Another idea would be finding an onsen, or staying in a ryokan.

https://en.m.wikipedia.org/wiki/Arima_Onsen

Recommended by my Japan expert friend, but I could not fit it in our schedule.

Nikko, north of Tokyo is definitely worth a day trip from Tokyo.
Also, near Kyoto, is Nara, which is work a day,

Nikko, a wonderful zen inducing destination...easy to get to/from Tokyo.

So what you really want is a smaller place in contrast to the cities. When I first read the post title I thought you meant something like to go to Korea also on the same trip.
We did a north to south travel in Japan last year and we did the Shimanami Kaido. You could do it in July. We did it in September. And let me say that September was hot. When we first got to Tokyo it was so hot and humid that it was extremely uncomfortable. We come from low humidity Colorado. We could not believe the humidity. We had to persevere however and soldier on.
I do not remember the heat and humidity being a factor on the biking on the Shimanami Kaido. Maybe by then we were used to the sweat fest. So if you are interested in that I would say go and do it. The bike path is very well marked and easy to follow. No worries there. You can easily rent and bike head on out. Even electric bikes. But we peddled.
Let me add that we did both Hakone and Nikko and they are hugely touristy. Hakone more so. But I think that people everywhere is a foregone conclusion in a place like Japan.

We did it in September. And let me say that September was hot. When we first got to Tokyo it was so hot and humid that it was extremely uncomfortable. We come from low humidity Colorado. We could not believe the humidity. We had to persevere however and soldier on.

If you had done your pre-trip research, you would have learned that June through September, and now even October, is "hot and sticky" time in Tokyo...plus October is the height of typhoon season in Japan. I once was in Tokyo in September on business, and it was miserably hot. i never again returned during the summer to early fall months.

I have been to Japan a half dozen times, and IMO your best bet at comfortable weather is April/May...cherry blossom time is nice, too, keeps creeping earlier on the calendar due to climate change, but it now happens in March (however it can quite cold in March. On a trip to Japan about 20 years ago, we saw the cherry blossoms in Tokyo in late March / early April, and it snowed on us in Kyoto).

There are websites with the historical record of cherry blossom peaks. The good news is that during March to early April, somewhere in Japan will have the blossoms, so if you plan a trip to Japan, with some flexibility you will find them...but Tokyo is quite special for this annual event.

Cherry blossom season is all well and good. Weatherwise. However, we only booked two months out from when we left. We rarely would book any trips out more than a few months. Not our style. If we do book out longer we end up taking another trip in the interim.
I was aware of cherry blossom season in Japan, but it was far away per the calendar. After the post above I did look it up and the first thing presented was - incredibly crowded, and "hordes".

I took a "first-timer" to Honshu this past summer - late June, early July 2024. This was the only time my travel partner had available. As you know, prepare for the heat! I brought UV umbrellas which we used frequently. Tokyo was worst for the heat for us - Kyoto and other areas were quite tolerable.

Did I miss how many days your intermediate stop would be? The below may not work if you have only one day.

We visited Kanazawa in between Kyoto and Tokyo. The trains work OK even though on the map the detour isn't as obvious as a possibility as somewhere like Hakone. Kanazawa Garden is fabulous, good market (and I don't generally like markets - been there done that as an expat), samurai and geisha districts. If your break is longer, there are day tours to Shirakawa and Gokayama that I can recommend - easily done.

As regards Nikko, we visited on a week day. The area is large so tourists are widely spread, but it was definitely full of tourists. We choose to walk to the shrines from the station rather than join the over-full bus and didn't try to get to the areas with the waterfalls.

I love Hakone - visited twice within the last 18 months. I avoided it for the summer, however. It was full enough in my spring (pre-cherry blossom) and fall (pre-autumn color) visits.

I was aware of cherry blossom season in Japan, but it was far away per the calendar. After the post above I did look it up and the first thing presented was - incredibly crowded, and "hordes".

The cherry trees are all over Tokyo, in parks, green spaces, etc. You do not have to be in a horde of people to enjoy them.

The Nakasendo trail is lovely. We did that in November 2018 and enjoyed it so much we are returning next November. This was the height of kōyō (fall color season) but it was not the least bit hectic or crowded. I have no idea what it would be like in July, but I doubt there would be more people than we saw.

https://www.japan-guide.com/ad/nakasendo/

How much time do you have? It needs 4-5 days to walk the popular section through Kiso Valley and Maggie area. We went with a small guided group, so I cannot help you with travel and lodging logistics. The US small-group tour companies do not offer this in summer, only in spring and autumn, but I see this Japanese company offers the Nakasendo in July and they have some availability:

https://walkjapan.com/tour/nakasendo-way-the-kiso-road

And of course there are companies that will help you set it up as a self-guided walk (hopefully with luggage transport for you).

If you don’t have that much time to spare for your “vacation”, you could consider visiting Naoshima, the so-called Art Island.

https://uno-hotel.com/en/

This could be a 2-night stop on your way south from Kyoto to Miyajima. You would leave the Shinkansen at Okayama and take a little train 45-55 minutes down to the port city of Uno, where you catch the ferry for the short ride to Naoshima Island. When we did this last November, we spent the first night in Uno at this nice modern hotel with a fantastic breakfast:

https://uno-hotel.com/en/

The next morning we caught the ferry over to Naoshima to spend the day and the night there. I booked the Benesse House hotel on the day reservations opened up (I think 6 months in advance). It was expensive, but well worth it.

https://benesse-artsite.jp/en/

The hotel shuttle met us at the ferry and carried us to the little town of Honmura, where we spent half the day exploring the Art House Project before meeting the little shuttle to take us to our hotel.

https://www.japan-guide.com/e/e5479.html

Our luggage was waiting for us in our room, and we had the rest of the afternoon to relax, stroll the beach, and admire the sculptures here, before a delicious French-inspired dinner in the hotel restaurant (included in the package).

We spent the next day exploring the Benesse area museums, including architect Tadeo Ando’s Chichu Art Museum, designed to display marvels like 5 large Monet paintings in totally natural light.

https://benesse-artsite.jp/en/art/chichu.html

This page has a fairly complete list of all the art museums and installations, some of which are on other islands:

https://benesse-artsite.jp/en/art/

Take particular note of the Bath House, which might be fun, if you enjoy this aspect of Japanese culture (I do, my husband does not):

https://benesse-artsite.jp/en/art/naoshimasento.html

https://japanjourneys.jp/kagawa/naoshima/attractions/i-love-yu-bathhouse-sento/

I think I have just talked myself into putting a return to Naoshima on our itinerary for next November.

So what you really want is a smaller place in contrast to the cities.

Treemoss2, that's exactly it!

Thanks for all the ideas everyone. We have 4 nights to spend on this "break" in total.

We did consider Hakone and Nikko and I guess 2 nights in each place might still be on the table. People seem to love Nikko, but was it a relief from the congestion? (I will avoid the bus to the falls as it seems that's a nightmare when it's crowded)

I think the draw of Hakone for us was a more nature-y vibe. I like the idea of the round course but not if it's jam packed. If we did go we'd stay 2 nights to get a super early start.

Lola-

Thank you for all the excellent suggestions and for your feedback on the Nakasendo. Which tour company did you use if you don't mind my asking? I actually was looking at the one you posted a link to bc they are the only ones who go when we're traveling (that I found.)

Were you left carrying packs during your walk or was your luggage transport daily (ie you we're just Able to carry water etc...)

I will look into the Art Island next!

People seem to love Nikko, but was it a relief from the congestion? (I will avoid the bus to the falls as it seems that's a nightmare when it's crowded)

Nikko is touristy, but in no way would I call it a "nightmare" crowd scene. Tokyo is a metro area of 30 million people, so yes, it is a crowded big city (but I love it). Nikko is a small town in a remote area of Japan.

One suggestion: looking at your first post, rather than looking for yet another destination for a 2 night stay with 2 added travel days, spend more time on Miyajima instead. I recommend 3 if not 4 nights for Nikko anyway; even traveling from Tokyo to Nikko, it is a long day, and not really worth it to me to go there on the itinerary timing you have.

As I indicated above, I enjoy Hakone - especially the nature vibe you note. I like hiking/walking - the route between the Amasake Chaya Tea House and Lake Ashi is scenic and historic, the Onshi- Hakone Park on Lake Ashi has scenic strolls, and the Hakone Shrine area also is attractive for walks. None of these is rigorous, but the Tokaido Road trail from the Teahouse needs care on the cobblestones, especially when slippery. I included multiple of these walks in one day. The Tokaido Road hike can be expanded back toward Hatajuko - I opted for the section promoted as "most scenic". https://www.japan-guide.com/e/e5205.html

In my two recent multi-night stays, I found taxis to be a good way to circumvent some of the crowds, queues for bus lines, etc. You can check the transit timetables on this link - pick a tab such as Tozan Cable Car - scroll down and you will find the timetable. The info is also available on the Jorudan or Navitime Travel app. - I found the apps to be very accurate and used it when on site and for planning from the US. The round course routes do have definite time limits - for instance, cable car started at 9 AM and ended at 5 PM, buses didn't begin runs before 10 AM when I was there. Thus, the taxi for me on several occasions. (or rent a car which I didn't do)
https://www.hakonenavi.jp/international/en/around

I rode various segments of the round course on multiple occasions. It can easily become jam-packed, particularly the cable car between Gora and Sounzan. Hardly room to breath on some occasions when I used it to return to my hotel. Same with the buses. I was never able to sit, no matter where I picked up a bus. My dates were "low" season, I do not know the numbers visiting Hakone in summer.

Comparing Nikko and Hakone, although not on the same trip and different times of year, I would say Nikko felt less crowded. Hakone's advantage is that it is directly between Kyoto and Tokyo. I suspect without looking that Nikko is accessed with transfers via Tokyo.

Here is an “off the beaten path” place I found while poking around websites for nice quiet places to visit between Tokyo and Kyoto. Nozawa Onsen is a popular ski resort near Nagano, but they are developing some summer tourism, with lots of hotels and good restaurants due to the winter visitors. The village itself looks charming, and there should be nice hiking in the hills, plus the “Stamp Trail” if you like treasure hunts. And lots of Onsens for relaxation.

https://japanjourneys.jp/nagano/nozawa-onsen/japan-journeys-style/stamp-trail/

https://www.nozawaholidays.com/news/nozawa-onsen-summer-activities/

It won’t work for us in November, but looks like a possibility for July, especially if you want to avoid Hakone-style crowds.

I see I did not answer your question about what company we used for walking the Nakasendo. We went with MT Sobek, an American adventure travel company based in Berkeley. We have used them for Patagonia, Tour du Mont Blanc and the Kumano Kodo trail in Japan as well. Great company but their Nakasendo Trail guided walk would not work for you as it is 9-10 days long and includes Kyoto and Tokyo as well. Plus they do not offer it in July. That Japanese company I linked does offer Nakasendo in July, and it is a 4-night/5-day tour that might fit your schedule. There may be other Japanese companies offering guided walking there in July as well.