There's a hard limit on how frequently you can run trains, because you need to maintain safe separation distances. Try to pack too many trains into the timetable and the whole line is just one tiny error away from grinding to a complete halt, or worse. There are some tricks to pack in slightly more trains, but they generally require expensive and disruptive signalling upgrades. For commuter lines with lots of closely-spaced stations, the most effective way of increasing train throughput is to reduce dwell time at stations and ensure punctual departure, hence the often rather brisk attitudes at Japanese stations during rush hour.

There are several limits on the length of trains, but the primary one is platform length. It's no use running a 7 car train if all of your platforms are 6 cars long - anything you might gain in capacity per train is wiped out by increased dwell time. You can extend platforms, but it's expensive, disruptive and only works if you have sufficient space at all (or practically all) of the stations on the route.

Japan can't really justify major rail investment, because passenger demand has been steadily declining for decades. Peak-time trains get progressively less busy every year, simply because there are fewer commuters every year.