JR East's recent announcements regarding service changes / cancellations to Tohoku / Akita Shinkansen from November 8th until further notice, and one of the more interesting changes is that the Hayabusa 15 from Tokyo to Sendai will be served with a single E6 set instead of the usual E5 sets.
https://www.jreast.co.jp/press/2021/20210927_ho02.pdf>>1713718>Implying Shinkansen didn't essentially kill most mid-distance air travel in Japan and basically became mainstream for mid-distance intercity travelAs for your question I'd say either JR West's Special Rapid or JR East's interurban that goes from Odawara / Atami through Tokyo to Takasaki / Utsunomiya as the "best" interurban trains in Japan.
JR West's Special Rapid from Tsuruga to Banshu-Ako:
https://www.youtube.com/watch?v=wdyoltRziywJR East's interurban from Atami to Kuroiso:
https://www.youtube.com/watch?v=nPKTMUAksqw 