NYT has a great writeup on the East Side Access tunnel. In short, the costs work out to 3.5bn/mile (!), there's ~200 "ghost" workers, and the usual spot of corruption and favoritism. It's a mess, and the MTA is deferring regular maintenance to pay for it.
https://www.nytimes.com/2017/12/28/nyregion/new-york-subway-...