The subway is what the subway is, it will never be nice like more modern foreign systems. 5,000,000 people take it a day, and they seldom replace any key infrastructure, it would just be too expensive. The crime is up, but if you were around for the 80's or early 90's, it feels like that.
The city is due for one of those periodic resets that happen occasionally, whether it will happen is anyone's guess. There isn't much working / middle class left, and they're the main driver of such things.
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Neat little doc on the subway in the 90's.
