Shinjuku being as concentrated as it is, is mostly a historical accident. Prewar Japan prohibited mainline railway options inside the Yamanote ring, because old steam railways took up a lot of room with yards and were very polluting; and and so you have all the suburban and long distance railways stopping or going around the ring (the notable exception being the Chuo Line which was built before that regulation). And the flattest, largest, and most attractive land development areas were west of the Yamanote ring so most trains ended up at Shibuya, or Shinjuku, or Ikebukuro, which round out the top three stations in Japan. This led to a lot of problems as these stations became more overcrowded with people changing from mainline suburban trains onto local transportation services. The through-running subways of Tokyo were developed largely to fix this, by allowing trains to pass through into the formerly prohibited city center so that people would stay on the same train instead of clogging up the platforms and stairwells and passageways by transferring. As more railways were able to through run, that lessened the need for yards to store trains that were no longer terminating, and they became large parcels of redevelopment that begot even more ridership.

To some degree, future planners learned from this by not overly concentrating passenger flows at a handful of stations; and by the time they were rapidly urbanizing, trains had become electric and there wasn't really any good reason to stop trains from entering central cities anymore. If you look at the Seoul or Beijing or Shanghai networks, they are intentionally a large, overlapping grid with many transfers to reduce the load on any single station.