The impressive, extensive and reliable Japanese railway systems does have many flaws. Some are infrastructure and some are financial.
There are two national track gauges. The standard 1435 mm gauge used for the dedicated JR shinkansen lines and some private railways including the Keikyu and Keisei operating around the Greater Tokyo area. The 1067 mm Cape gauge is used across the entire JR network away from shinkansen network, as well as on many private railways. Despite some trials, there is no rolling stock which uses either track gauge - and the two works remain entirely seperate. Some JR 1067 mm tracks have been re-gauged to 1435 mm gauge in northern Honshu as part of mini shinkansen project.
Japanese railways feature many level (at grade) crossings, where road and railway cross on the same level. By default, barriers left open for road traffic and then closed for passing trains. The famous Shinagawa No 1 Crossing on the Keikyu main line is frequent closed for road traffic, allowing unhindered passage of the busy passenger service.
Back in 1987, the nationalised JNR was privatised - mainly to deal with the extraordinary debt problem. Nearly forty years later, and this is still not resolved. The privatised and restructuring separated the healthy railway businesses from the legacy liabilities, allowed the new companies to thrive. But left the government to deal with much of the old debt over several decades.
The strategically import JR Freight company usually breaks-even, occasionally making modest profits. The freight operator does not generating the huge returns seen on the passenger Shinkansen networks.
The JR passenger group has six operators. Two are still in state hands: JR Kyushu and JR Hokkaidō, while the other four have been privatised in recent decades. Each JR passenger company has expanded into other business interests. But there is no competition between them, with each having a regional monopoly. There are no open access operators - as in Europe. And unlike Europe, there is little dynamic pricing - with the same fare regardless of time of purchase or time of travel.
Yet, Japan is an excellent country to explore by train. I know. Across four visits, I’ve visited all four islands with railway networks.