This is the real reason for all of these problems. It's political. The fares don't come close to covering the operating and capital cost of the system. It's not

This is the real reason for all of these problems. It's political. The fares don't come close to covering the operating and capital cost of the system. It's not user-pays, it requires constant government subsidies (as an implementation detail, the required government subsidies form a convenient way for the state and city to hold each other hostage, but that's another story). Any talk of use pays is met with outrage about how low income people out in the boroughs couldn't afford it, so the whole system continues to operate as a horribly inefficient welfare system for poor people to get to underpaid jobs in the city, instead of a transit system. It would help a lot to double (triple?) the fares overnight, and give the poor people out in the boroughs a free metrocard - at least that way you're capturing the value provided to the rich people and tourists all the way through manhattan and brooklyn.