No argument about the expenses of renting a car, especially if you plan on travelling intercity. The expressway tolls is quite high.

There are many inexpensive alternatives if speed is not critical.

The intercity kousoku bus costs around 5000-8000 yen one way from Tokyo to Osaka. Since the buses runs overnight, people on a budget can save a night of lodging and not have travelling time cut into day time.

The slower trains cost around 8500 yen from Tokyo to Osaka, but it will take you 9 hours to make the same trip that Shinkansen makes in 3 hours. Is your 6 hour with the 6000 yen super express surcharge? It can cost even less if you travel during promotional periods when you can use the Seishun 18 kippu.

JAL and ANA offer air passes to the passengers of their respective alliances. LCC also exist in Japan. Skynet and AirDo comes to mind, though I have not yet flown on them.