I set off to make good use of an unexpected string of days off and see some of Japan that is usually not seen by those focused on going from A to B, and I feel that I succeeded in that. The local trains through the mountains provided some incredible scenery, and had it been hiking season (for someone who does not have their winter hiking gear at hand) I would have loved to have stopped at several places along the way and headed deeper into the landscape.
Would I do it again? Yes, but I would do it differently. Most significantly I would avoid the Tokaido line; with bullet trains (shinkansen) departing along that route (on dedicated tracks) every 10 minutes or so there is no real need for anything other than pure local service from one shinkansen station to the next, so there isn’t. Perhaps if one were to go through the tea gardens of Shizuoka at noon on a cloudless weekday the scenery in that section might be worth the fewer tunnels and slower pace of a local, but otherwise expect a long, crowded, and uncomfortable ride through strings of minor cities. Likewise the departure from Tokyo to Takasaki would be a contender for a shinkansen to get out of the city quickly and maximize time in the places where the scenery from the twisty tracks of local trains outshine the tunnels of the shinkansen.
If I were eligible for a Japan Rail Pass my approach would be to make use of the shinkansen to cover less scenic distance quickly, then use the limited trains where possible to get the more comfortable seating and speed they provide along the more scenic local tracks – particularly if going to Takayama. That said, the local trains do carry a mixed cross section of society and the people watching can be quite entertaining as well.
I was warned that it could be difficult and uncomfortable. The warning was partly correct. To follow the warning would have been to miss far too much.