The premise is basically that Tokyo is the busiest city on planet earth and so should therefore have the best public transit and pedestrian infrastructure by a huge margin, when in fact it still gives unbelievable space to cars (Shibuya crossing should have been permanently closed to cars 20 years ago).
As for trains, during rush hour trains can be so full you might be squashed against the door unable to move - incredibly unsafe, leads to daily injuries, and some argue have something to do with the heinous levels of sexual assault on trains. Not to mention even in Shinjuku station most platforms don't have guardrails to prevent accidental or purposeful death by trains, another outsized problem in Tokyo.
But the most glaring issue is around the very design of the system. Privatization results in requiring riders to sometimes exit a station of one company, go all the way up to ground level, walk a block or to two another different company station, and then ride another train. A government managed system wouldn't have this issue, it would simply combine the stations at design time.