I completely agree with the others. The Shinkansen network now stretches from Kagoshima on the southern tip of Kyushu to Aomori, on the northern end of Honshu.

Buy a Japan Rail Pass (the vouchers must be purchased outside of Japan), and you can hop on and off all but the super-fast Shinkansen at will without paying extra, even make reservations. Most cities have such good public transit or are so walkable that you don't need a car. Even some of the rural areas are well-served by buses. In 35+ years of traveling to Japan, including to some very remote areas, I have never rented a car nor felt the need for one. That's how good the system is.

I've taken intercity bus trips that run on the expressways. "Boring" and "ugly" are the words that come to mind.

You may come from a place with poor public transit so that driving is what occurs to you first. But you would be missing one of the best aspects of Japan if you didn't take advantage of the train and bus systems.