You can take a train to nearly every corner of japan. Japanese cities make sure you have a parking spot before you can buy a car. There is very little on street parking so many streets are open. The streets are narrow and often able to be shared between pedestrians and slow traffic. Roads specifically meant for cars are often seperated from pedestrians.
Japan has done a lot more than most other countries. Rural areas will always be more difficult to service due to their density but i still think japan has done better there than most.
Thier housing culture also makes it easier to move where you want to, which should make moving from rural to the city more feasable for those whom can't handle the rural lifestyles.