what are some actual hidden gems in japan?

Aside from all the overrated places they hype up on tiktok as "hidden gems" i want to find some actual hidden gems.

I'm currently planning for my first 3 days of my trip to be away from the crowds and immerse myself in nature but also interested in visiting some edo villages, maybe a samurai residence or anything related, and temples with views, etc. Preferably somewhere outside nagoya that i can drive to as ill be renting a car for 3 days and later will be staying in kyoto for 4. I'm open to visiting some prefectures near nagoya or kyoto as well. i'm already planning on visiting magome/tsumago post town and ryujin waterfall but having a hard time deciding on planning the rest of my trip. Im not interested in visiting gero onsen and takayama as it will be the end of november so i want to avoid the alps and save that for a summer trip. Also if you have any suggestions on good spots to visit in the end of november.

Outside Nagoya and driving, then Meiji Mura is worth a visit. Not a hidden gem as it is in plain sight, but the location makes it less visited than many other places and something that 99% of international tourists never get to experience.
Real hidden gems are those discovered by exploration. I spent time today trying to explain that to my current group. Yes, they will get some, but they will be along the way and often unexpected and not necessarily planned as we make adjustments to our travels. (like today dealing with a rainy Tokyo day)
Even in big cities, what you might consider a "gem", others wouldn't be interested in. While I have visited Nagoya (as an example) many times (not as often as my usual work destinations), my personal preferences and items that excite me, might not appeal to the next person.
And, sure, you might avoid Takayama, but the city has a lot, and those I share with my guests. Most recently we were hunting tools - specifically a gardening tools and in a major homeware store we visited (not on the tourist trail), but I knew my guest was left handed from a single comment they made, and found a left handed version in an obscure garden center later that day.

As the last poster mentioned - the idea of an 'actual hidden gem' is very subjective. I've been to temples in Kyoto during the off season and I'm almost the only person in a huge complex. Then I've also visited during koyo (fall colours) or hamani (cherry blossoms) and the place is absolutely packed.

In general - I find Open Air Museums in Japan to often be quite interesting. Meiji Mura is absolutely huge and will either amaze or bore you depending on your interests. Just make sure you have good walking shoes as the place is absolutely huge. I'm also a fan of the Tokyo Open Air Museum as well.

I also don't want to burst your bubble - but a very quick search of locations near Nagoya on Japan Guide will give you lots of potential places to visit. I've also posted stuff on around half of my travels in Japan here: https://www.japan-guide.com/community/mfedley/

Something that is not a hidden gem but is massively overlooked in Nagoya is Higashiyama
Zoo and Botanical Gardens. The huge botanical garden has lots of traditional buildings scattered around it and you can even visit some old residences including I think some Gassho huts.

https://www.higashiyama.city.nagoya.jp/english/

For me - Nara and Shiga Prefectures probably have the most hidden gems if we are talking close to Nagoya. Also - the Kiso Valley is nice but is reasonably touristy. The Kumano Kodo for me is a bit more special but is also much more rugged.

It is not a hidden spot for Japanese people, but Korankei is a famous spot for autumn leaves.
https://www.aichi-now.jp/en/spots/detail/1021/
I have read a book about Asuke's town planning and I am interested in Asuke. http://asuke.info/event/nov/entry-3035.html

Kawami Shikizakura no Sato, which was listed in the tour content on the page I linked earlier, may also be good.
https://www.kankou-obara.toyota.aichi.jp/place/174/
https://www.aichi-now.jp/en/spots/detail/132/
https://www.kankou-obara.toyota.aichi.jp/english/shikizakura.html

↑
Sorry.
×Kawami Shikizakura no Sato →〇Semmi Shikizakura no Sato

WIth a car from Nagoya, the Kii Peninsula (or maybe just the eastern side) would be good. I wouldn’t expect Edo villages or samurai residences, but Ise Shrine is worth a visit, and you could go to Toba if you like the ocean. Continuing westward the peninsula, there are some great hikes on the Iseji section of Kumano Kodo. And plenty of places to sightsee and relax as far as you want to drive. I probably wouldn’t do a circuit of the entire peninsula in only three days, but you could.

You might get some ideas from the following Japan Guide article from a while back:
https://www.japan-guide.com/ad/central-japan/190318.html

The following writeup might also have some ideas beyond the main subject of the article:
https://www.japan-guide.com/ad/shingu-city/

But if you look around you can find lots more ideas. I was recently researching a hike on the Matsumoto Pass from Kumano City (Kumanoshi) and noticed that their tourism page has some other suggestions for nice places to visit around there, and it looks like there is some lodging in town that could be good. I’m not sure if they have an Engish page or not but you could use a web translator I guess.
http://kumano-kankou.com/

That area does tend to get a lot of rain, so you might want to have some contingency plans. In late November you will probably get pretty good weather but you can never count on it. If it rains, it will be COLD….

The Ashizuri Underwater Aquarium:
https://abandonedkansai.com/2024/05/17/ashizuri-underwater-aquarium/