That said, the MTA has a serious cost problem. Their projects are routinely way over budget and massively delayed. The 7 extension and east side access (LIRR) projects cost considerably more per km than any rail project anywhere in the world. Yes, they are complex but so are many other projects (e.g. London crossrail).
It's not any one underlying problem, but the byzantine MTA governance structure makes it hard to address all of them.