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Shirakawa Go is definitely a place to visit but I probably wouldn't want to stay overnight.

I did spend the night in Hakone to experience a Ryokan. It might be a place you wish to stay for two nights.

How are you traveling? Car? Train? Bus?

If we go to Shirakawa Go, we would stay in Takayama. Most likely travel by train

Nikko was awesome.

We stayed in a ryokan at Takayama and enjoyed it. It has a nice old town to explore But I haven’t been to the other places on your list for comparison, so can’t say if it’s the best choice of those.
We also like nature and smaller villages - of the places we went to on our trip on Honshu, Tsumago, Magome and Narai were the nicest, also surrounded by nice walking trails.

Agreed Nikko would be a great 2 day, 1 night trip - but in the wrong direction by train. I have not stayed at most of the others you listed, but recently wound up with 2 days, 1 night on Lake Ashi at a very nice hotel with onsen, Mt. Fuji views, cable car, and nice walking. It was on a Shinkansen route Kyoto to Odawara, then Odawara to Tokyo (with a one hour free hotel shuttle from the train station to the lake and hotel).

I'm glad you clarified Tamayaka for Takayama. I liked Takayama. The historic old town was interesting to explore.

Considering when you are going, Hakone is on a lake and it might be cold by the time you get there. If there are Ryokans that you like in Takayama, I'd suggest looking into them. That way, you could experience a Ryokan and visit Shirakawa-go.

Make sure you are leaving enough time for Kyoto and surrounding places like Nara.

Thanks everyone. Deciding between all these options is the hard part. Not trying to compare Mt Fuji to Rainier- but I live in Seattle and realize that if there is cloud cover, it might be tough to see the mountain.
Would love to see traditional villages and the alps, which I why I am torn about Takayama/Shirakawa-go.
Sounds like Nikko and Hakone are easier to get to?

Wow thank you for all the information! Really appreciate all this!

Kamakura has nice Ryokans and great walking trails and small temples. it may be worth an over nite
Hakone would be your best - it has beautiful Ryokans, boat rides on the Lake, Outdoor Picasso museum. Hakone is very famous for their Onsens. Beautiful views of Mt. Fuji

Nikko is beautiful but hard to get to and lots of stairs to all of their temples.

Enjoy!

How about stopping along the Nakasendo Trail and visiting 2 post towns, Magome and Tsumago? You would take the Shinkansen to Nagoya, and then a more local train to Nakatsugawa. Either bus or taxi to Magome 30-45 min away, spend time to exploring Magome, and then hike about 7 km to Tsumago. You are in rural Japan. After exploring this more sleepy post town, spend a night at Takimi Onsen. The owner picks you up from Tsumago and his place is located in the woods 15-20 min away. The highlights are - you are the only group in this traditional home, complete with separate indoor and outdoor onsens for men and women which overlook the woods and some waterfalls. Lots of original artwork, crafts, decorations in this rustic home. Spotless clean as is everything in Japan. And best of all the kind owner is a retired chef from one of the big Tokyo hotels and cooks an amazing traditional dinner and breakfast. In the morning he will drive you to the nearby train station where you catch 2 local trains to get back to Nagoya and then the Shinkansen to Kyoto. I found the Really Rural Japan website really helpful and found the owner Michael very responsive to my email queries. We booked a day tour Magome-Tsumago with his associate Sachi - unfortunately it was pouring rain - but the mountainy rural area was still very beautiful. We were just there 2 weeks ago and did this trip from Kyoto..