I empathize with the MTA a bit. It's an old system that is probably underfunded and operated by a very strong union which costs a lot of money. There are still parts of the system that no manufacturer builds for anymore requiring staff machinists to custom make parts.
The signaling system is ancient and any real effort to modernize it (like on the L line) is fought by the union which considers modernization a threat to jobs.
Lastly, it's a system that runs 24 hours a day which almost no other train system can claim. finding times for the appropriate maintenance is very difficult and requires all the rerouting you tend to see on the weekends. People litter so much more in NYC than they do in other major cities across the world in my experience and litter on the tracks causes so many issues. And there's little to no time to clear litter daily off the tracks.
The system is underfunded, oversubscribed and outdated.
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