I think I'm split on this project.
At this point, non-car infrastructure of this scale getting finished is such a rarity (maybe once every two decades or so) that I'm glad it happened. Plus, this adds major system redundancy, which is something that America has a lot of trouble fathoming the importance of. The author does acknowledge this, but I don't think he grasps just how crucial it is for the country's busiest railroad to have a second way into NYC.
OTOH, just about every aspect of this project, from planning, to execution, to opening, is embarrassing.
All that said, once these projects get finished, public memory of how bad they are lasts anywhere from 5-10 years. After that, people are just glad the infrastructure exists in the first place.