At the point the system is right now, perhaps the only way forward is CBTC. I don't know the details of subway operations and my observations are from being a regular subway rider. The current crisis, in my opinion, is the result of the TA's knee-jerk reaction to accidents and incidents that have occurred over the course of the years and their overzealous approach on safety. Because of this approach, the effects those measures had on capacity were not taken into account until they had an adverse effect on the subway actually being able to run the scheduled trains, be it because of timer proliferation, ridiculous terminal procedures, lax attitude by RCC on how much service is actually run vs scheduled and overcautious train operators coupled with the slowing down of trains themselves.
We now have a subway network that is riddled with timers that have effectively destroyed capacity potential. And this is were CBTC will actually help, I believe. Because it will give those overly cautious train operators more confidence when manually operating the train, instead of them relying on strict unmaintained timers which slow them down even more then they "have" to. The MTA has to, at this point, look at and follow best practices from all over the world so that it can improve on its basic day to day operations and make them worthy of a system that carries over 5.5 million people per woking day. The NYC subway can no longer be the exception. By switching to CBTC there would be less moving parts in the signaling system that are prone to failure, train speed would be precisely and accurately regulated the subway would be much closer to optimal performance than it is today. These are my thoughts of course.