I think the best way to describe it is that it sucks either way to commute in Tokyo no matter what means of transports you end up using, except if you can live very close to your office, which is not the experience of 99% of people.
Commuting in Tokyo is not without problem, but consistently better than commuting anywhere else I've been.
Also, you seem to completely ignore the point that the alternative "everyone commutes by car" (or you have other alternatives?) would result in a constant gridlock given Tokyo's scale - so it would be orders of magnitude worse.
I challenge you to find a mechanism that works for this and is quick enough to keep up at rush hour in the average Tokyo train station.
Additionally, people move at different speeds through the station due to factors like age, familiarity with the network, disability, bladder capacity etc.
It’s a non-trivial problem to solve, and likely only marginally improves user experience.
I suspect the reason this isn't valuable is that the feedback loop is already pretty good at high occupancy rates: when one car is at capacity, every other car is too.
Not to mention the trains stop every minute or two, and people don't, like, book that stuff ahead of time.
And they already know which train routes at which times are crowded, if they could just add more capacity they'd have already done it.
- which cars are normally less crowded
- which cars are recommended for getting off at a certain station, based on proximity of the exits at that station to each car
Google Maps (as well as other apps) also show similar information when asking for transit directions (for the former it only gives you the average on the whole train, not by car)
The feeling of independence (or not feeling like “cattle“) is substantially reduced in big cities, where you are subjected to a lot of traffic rules, overcrowding of cars, jaywalkers, accidents, potholes, diversions, expensive parking space... I could go on.