Tokyo metro is like a quarter of the population of Japan. Japan basically is Tokyo, to a degree that probably isn't matched by any other city / nation on Earth. Even if you insist on just looking at the 23 wards it's a big deal - 7% of the population lives in one of the 23 wards. That's like if 22 million people lived just within the one of the five boroughs of New York. (Comparing Tokyo metro with New York/Newark metro, imagine if 80 million people lived there, and how that would affect the influence of that area on the economy of the US.)

To suppose that Tokyo can go in one direction or stagnate while the rest of the country goes in another direction and prospers is just totally unrealistic.