Nothing is perfect, not even Japanese trains, but in my experience, the grandparent poster is closer to the truth than you are: Japanese trains are paragons of time-keeping ("paragon: a model or pattern of excellence or of a particular excellence").
Obviously right after a typhoon is a bad time to measure anything, but in normal operation, Japanese trains are extremely punctual, to a degree that's downright astonishing to anyone used to trains in most other countries. Arriving more than a minute late is unusual (less than that is hard to judge because the timetables don't include seconds).
The only real exceptions are situations where it's almost impossible to do better—cleaning up after a suicide (and here they're still many times faster than in the U.S., for instance), or operating in inclement weather so severe that attempting normal operation would be dangerous.
These exceptions do happen often enough that anybody who lives in Japan will be inconvenienced occasionally (with suicides being the main offender), but 99% of the time, you can set your watch by train arrivals.
More to the point, there seems little they could do to make punctuality much better, unless they can figure out how to cheer up the population to the point of discouraging suicides (and of course they are actually working on this issue by moving to platform doors on some lines, not to mention more wacky methods like the blue lights underneath the ends of platforms).
If something is so good that there's little practical room for any improvement, doesn't that make it a pretty good candidate for being called "a paragon"?
Slightly off topic, but when my brother was young he became obsessed with preventing train suicides and we actually came to the conclusion that placing an airbag on the front of the train would most likely (help to) resolve this issue.
Based on our calculations it should be feasible to prevent death in at least a few percent of cases.
Given that the biggest draw for train suicides is its near 100% success rate that would probably quickly reduce train suicides by a very significant factor.
I also thought this is an almost impossible problem to solve, until a friend pointed out that on the Jubilee line extension (London Underground), it is solved.
The edge of the platform at the newer stations is walled off from the track by glass. The platform doors line up with the train's, and open/close at the same time. So there's no access to the track at any point, hence no opportunity for "person under train".
They have those doors in many places in Asia also, but most of the trains people are jumping in front of in Japan are above ground and the stations are literally just platforms with a roof.
Platform doors are certainly possible above ground too.
Usually in Tokyo, they use chest-height barriers/doors for above-ground lines, e.g. currently the Meguro-line has these, and in the future, the Yamanote-line will. This doesn't make suicides impossible, but makes them more difficult to a degree which will certainly discourage many people (you can't just fling yourself off the platform at the last moment). [Some subways, e.g. the Fukutoshin-line, use these as well.]
A more problematic issue is stations which handle many disparate types of trains on the same platforms, which makes it much more difficult to achieve the consistent door positioning you need for platform doors.
As a guy sitting in a soba joint in Tokyo right now...I cannot imagine how much it would cost to put those doors on all the JR and Metro stations. It's certainly in the realm of prohibitive.
They do end up saving some money too, though, not only by reducing suicides and accidents, but because platform doors seem to be considered a prerequisite for "one-man operation" (ワンマン運転) on most lines, and that can help reduce staffing costs.
Most Tokyo stations also have high enough ridership that such capital improvements are a lot easier to swallow than they would be for "concrete slab in the countryside" stations.
Luckily, it's the sort of thing they can do incrementally in the places where it makes the most sense; no need to do every line and every station immediately. I imagine they'll probably continue to do it slowly, just as they're slowly adding elevators and other accessibility improvements to even minor stations.
Obviously right after a typhoon is a bad time to measure anything, but in normal operation, Japanese trains are extremely punctual, to a degree that's downright astonishing to anyone used to trains in most other countries. Arriving more than a minute late is unusual (less than that is hard to judge because the timetables don't include seconds).
The only real exceptions are situations where it's almost impossible to do better—cleaning up after a suicide (and here they're still many times faster than in the U.S., for instance), or operating in inclement weather so severe that attempting normal operation would be dangerous.
These exceptions do happen often enough that anybody who lives in Japan will be inconvenienced occasionally (with suicides being the main offender), but 99% of the time, you can set your watch by train arrivals.
More to the point, there seems little they could do to make punctuality much better, unless they can figure out how to cheer up the population to the point of discouraging suicides (and of course they are actually working on this issue by moving to platform doors on some lines, not to mention more wacky methods like the blue lights underneath the ends of platforms).
If something is so good that there's little practical room for any improvement, doesn't that make it a pretty good candidate for being called "a paragon"?