What makes Japan's rail system so effective is vertical integration. The country's seven major railway companies own the land around their respective lines and rent it out.
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Redundancy. Another key feature of Japan's transportation system is that it is built to grow and evolve. Rail lines are rarely single tracks, but often have three or four tracks to allow for express service. Subway lines directly connect with commuter rail lines, allowing for seamless service across regions.
Rail in the US is dominated by freight movements, the passenger sector is very much and afterthought and doesn't receive much investment. As a result their lines are slow, dominated by freight, and their rolling stock is old and low tech. Japan, in contrast, has one of the best and most modern railways in the world.
If China is the largest exporter of rail technology in the world, its neighbour Japan is certainly the most technologically advanced manufacturer on the market. Having launched the first class of bullet trains in 1964, the country has continuously updated its models according to the latest technological advancements.
While the US was a passenger train pioneer in the 19th century, after WWII, railways began to decline. The auto industry was booming, and Americans bought cars and houses in suburbs without rail connections. Highways (as well as aviation) became the focus of infrastructure spending, at the expense of rail.
During the post-World War II boom many railroads were driven out of business due to competition from airlines and Interstate highways. The rise of the automobile led to the end of passenger train service on most railroads.