The usage rates in Japanese cities are among the highest in the world, as are the punctuality and reliability of the intercity trains.

Could the system be less convoluted? Absolutely. But IMO most European countries aren't in much of a position to criticize given that they aren't even willing to step up to the plate to anywhere near the same degree, to say nothing of North America.

Now, one might argue that this has more to do with city form than it does with the quality of the PT infrastructure, but that is infrastructure too, and those two types of infra are two sides of the same coin. And yeah, the city form isn't completely perfect either, but when it comes to moving a greater proportion of people in the safest and most energy and space efficient way, the numbers are just higher than most other places.