A year ago, I participated as many others in the Metropolitan Transit Authority’s idea challenge on solving the signaling problem within a feasible time and less than the projected >40bn USD costs. Since a child, I personally experienced the subway on numerous visits and was always astound on what the subway managed to perform, especially in comparison to European counterparts from Paris or Berlin. However, over the last years, the vital transit system has more and more deteriorated.
A few reasons for this are explained in this video from the New York Times:

So what is to do (besides solving the debt and funding issues)? The following things come into my mind:

• Ownership of service, technology, expertise and work ethos among the staff to strengthen the culture of the organization and enable the people to solve one problem at a time
• Investing in technology and building custom made solution to solve the problems – avoid wrong compromises with off-the-shelf solutions since MTA is a big enough market to do it themself
• Found and fund small innovative organizations within MTA
• Insource most activities that have been outsourced