Hi there,
Always nice to meet someone with the same passion for trains as me, if there is any country in the world where you can take your time to enjoy train rides, then it is Japan, and the Japan Rail Pass is the tool to make it possible.
It is hard to give specific recommendations without knowing what you are in to, but I can certainly help you get started and hopefully share some inspiration. Trains that generally offer the best view are Ltd. Express trains and Joyful trains. I'm assuming you already have some knowledge here, but in short, Ltd. Express trains are faster intercity trains that come with comfortable seats. Joyful trains are excursion trains where the ride is the attraction as much as anything else. We cover several of this on our blog: https://www.jrpass.com/blog?tag=joyful-trains
The Shinkansen are super cool, and I highly recommend doing at least Tokyo - Nagoya on the Tokaido Shinkansen to see Fuji. At the same time, many Shinkansen lines have a lot of Tunnels (the Niigata Shinkansen line is notorious for this) and they are a bit less fun.
From Tokyo, there are plenty of good options, a few that come to mind:
- The Ltd. Express train between Shinjuku - Matsumoto
- The Hitachi from Tokyo to Sendai
- The Resort Shirakami, but it will take some time to get there.
JR East has a cool tool, to explore special trains and routes for inspiration:
https://www.jreast.co.jp/multi/en/traininformation/
For other places that come to mind where you could base yourself:
Kanazawa and is a great place to do trips from around the Japanese Alps, Matsumoto (just the train trip is worth it), Takayama and more.
Other options for a good base would be: Kyoto, to explore Kansai from, and even as far as Hiroshima. Or, go to Fukuoka, which is great for trips all around Kyushu, like Nagasaki, Beppu, Kagoshima and plenty of others.
Let me know what you think, and I'm sure that I can post some more :)
Kind regards,
Daniel