I am working on a trip to Japan in May with my wife who has never been to Japan. I want to give her a good introductory overview. I was thinking 4 nights in Tokyo and 4 nights in Kyoto/Osaka. Looking at 1 night in Hakone in the middle. I want to avoid obvious tourist traps. Any other onsen towns that would be more authentic that would be reasonable to get to? What midrange hotels? Temples to prioritize? I want to see some but my beef on European tours are too many churches. Is Nara worth the time? I have read previous posts so I have good dining suggestions.
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You may want to look at the small onsen and craft towns on the north central coasts of Japan that are now easily accessible with the extension of the Hokuriku shinkansen (bullet train) line last March.
It still stops about 60 miles short of Kyoto but that gap is covered by regular (non-shinkansen) expresses. The New York Times article linked below has lots of info.
Also, if you haven’t heard, you’d want to avoid going there in the first week of May. It’s one of the busiest travel time in Japan (“Golden Week”), with four national holidays between April 29 and May 5.
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Some of the best temples and shrines are already well known so can get hugely crowded. Go early in the day or late in the afternoon for the best experiences. Nara is definitely worth at least a day. Nagano has some good onsens.
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you are avoiding tourist traps by simply going to Japan LOL
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This is especially true in Kyoto. I went to Kiyomizu-dera at 6am, and there was already a (small) crowd. I can’t imagine what the area is like around Noon.
If you can wake up early, Kyoto is a lovely place to visit. Just embrace the fact that jet lag is your friend.
Also, Nara is very much worth going to, though the “deer park” next to the main road is a bit of a let down. But, if you go deeper into the more forested areas of the Nara Park, it is wonderful.
If you are in Kyoto or Osaka, a day trip to Himeji Castle is also a must. One of the few original castles in Japan that is still standing. Most of the other castles in Japan (including Osaka Castle) are reconstructions.
get there early
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I recently did a 10+ day Japan deal with a similar Tokyo > Hakone > Kyoto + Naoshima Island itinerary. If you are doing Hakone for one night (as we did en route to Kyoto) the best thing you can do is get a reservation for a visit here: https://www.odawara-af.com/en/
Have your hotel or wherever you are staying forward your luggage to whatever onsen you are staying at in Hakone. Take the train from Tokyo > Enoura Observatory (close to Hakone) and spend half a day there. I promise as “cool” as onsen’s seem, soaking gets boring…this place will change your perspective on life (on the other hand).
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If you guys are moderately serious art lovers then I’d second smbeatt’s recommendation of Naoshima - some truly astonishing art and architecture. It’s a bit of a hassle to get there but definitely worth the trip.
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Naoshima is a great idea. I haven’t been myself, but heard nothing but great things. And it’s the main location of a triennial modern art festival called Setouchi Triennale, which is on this year – its spring session runs April 18 (Fri) thru May 25 (Sun).
So a great time to visit though, at this point, the famous “art hotel” on Naoshima, the Benesse House, is likely sold out. But you can stay on the mainland side and commute to Naoshima and other islands hosting the festival.
FESTIVAL:
HOTEL:
I’ve thought about Naoshima in the past, but like others have said, it’s a little more difficult to travel there so it hasn’t happened yet.
My April Japan trip will comprise of Matsumoto, Toyama, and Kanazawa with a day trip to Shirakawa-go/Gokayama.
In May, I’ll be in Fukuoka again and I want to explore the other side of Kyushu so Miyazaki and Beppu will be in the cards. I also would like to visit Kitakyushu.
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My two nights on Naoshima coupled with the visit to Sugimoto’s ‘Enoura Observatory’ were the highlights of a highlight filled Japan trip. My mom and I stayed at Naoshima Ryokan Roka, where they had electric bikes for us that I took all over the island or a happy to drive us around van. If you are going to make the Naoshima journey, stay a couple nights minimum so you can do it all. 3 days would not be a waste (and you could even pop over to Teshima).
Happy to fill in more details. Naoshima was an easy train, cab, ferry journey for us from Kyoto.
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Thank you on the heads up. 
If anyone is gonna be in Japan in March:
Hello. This is Soga from Domaine Takahiko.
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[Event Information]
On Monday, March 17th at 7pm, a special collaboration dinner will be held at the Imperial Hotel Tokyo, limited to 12 people, featuring the Imperial Hotel’s 14th Tokyo Head Chef, Yu Sugimoto, Domaine Takahiko, and Domaine Mont.
On the day, Domaine Takahiko will have several types of wine available, including back vintage Nanatsumori.
Dinner personally prepared by Chef Sugimoto, the Imperial Hotel’s executive chef, is usually only available to one group per day, but this time, a special invitation will be extended to 12 guests only, who will be able to enjoy our wine and Chef Sugimoto’s course menu.
This is a one-night-only special event, with the head chef himself considering the pairings.
Come enjoy some delicious food and wine with us.
Reservations are now open.
Make a reservation here
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