Here's my 5 step plan to fix Japan:
1. Workday starts as soon as Takeshi leaves his house. Companies now have to pay a "transportation fee" for their employees so they can no longer expect an hour long Shinkansen trip to just be a fact of life.
2. Tax breaks for corporations who open new buildings to encourage them to create HQs more local to the non-Tokyoites.
3. Create "startup industries" via government mandate before privatizing them. EG: open up a factory in Kochi, hire locals, after 1 - 2 years of operation, the company becomes privatized with the ownership being split between the 10 most senior employees.
4. Create a "remigration tax break" that completely cuts the taxes -- for 5 years -- of Japanese citizens who move back to their hometowns. The tax break lasts as long as they live in that town.
5. And this is the most important one -- taper off Social Security by 10% every year for the next 9 years so that SS payments are capped at 10% of the current amount.

Japan's birthrate is far higher in the provinces than in Tokyo, Kyoto, Osaka, Hiroshima, Sendai, and Fukuoka. These measures encourage a decentralization of business outside of those cities and into the provinces, which means that ol' Joe Takeshi can obtain reliable employment in the countryside. The regular citizens are then given incentives to move into the countryside where they have more space and don't spend as long commuting to work. The currency will strengthen as Japan can start paying off its national debt due to lowered SS payments and increased tax income from higher employment and higher wealth generation from industry.

tl;dr: destroy the rat race and save the soul.