When you are travelling in the daytime, consider using the train to take a tour.
This will give you exceptional views of Mount Fuji when travelling to Tokyo from Kyoto, in particular if you are sitting on the left (which corresponds to seats in row E).
The same applies when travelling to Kanazawa from Kyoto
to see Lake Biwa (sitting on the left).
On local trains and on certain Limited Express trains, the train driver's cabin is see-through and provides panoramic views of the landscape. This is the place to be.
For example, when crossing the inland sea from Honshu to Shikoku, the first 2 seats on the right behind the driver provide an impressive view of the inland sea.