Trains not running well today, on the green line there's one running 5 minutes late. That's unacceptable by Japanese standards (and on-time by UK standards)...
If you have lived here or spent enough time you get a feel for the rhythm of walking and moving through what to outsiders looks like madness and complexity. However the reality is it is perfectly ordered. One or a few tourist can be absorbed but 1000s just makes it all break!
The only issue I ever had was determining the best exit at an unfamiliar station. Pick the wrong one at a larger station and you can find yourself a long way from where you were heading.
Also trust me, it is great you had no issues (engineer likely since you are on HN) and were able to see the patterns, however most foreigners are like deer in headlights.
Also exits are simple. Figure out where you want to be and on their website it will say what station and what exit. Their is alway a map when you get off a platform with the exits labeled.
Once you know to keep walking the platform to the exit you need it's very easy for most stations.
Where I struggled was finding a specific shop or eatery I had previously visited at Ueno. Too many separate concourses and shopping areas.
Green line is Yamanote line and neither Yamanote nor Chuo line are that late unless some serious accidents occur. If you mean by, 1-3m then, I guess you're within a reasonable claim.