Part of it is New York's system is much older than the rest of your examples, Tokyo didn't really expand beyond a single tunnel till 50s-60s, Beijing opened in the 60s and Shanghai only started construction in the mid 80s. Then on top of that the city of New York isn't actually in charge fully so (like just happened) if they try to do something disruptive but critical the governor can come and derail the whole plan. I don't mean to say it excuses the mismanagement but it does explain a lot of the problems.

Also it's not like they're not building new stuff in 2017 the second avenue subway opened with 3 new stations.