The article specifically calls out nuisance lawsuits, inexperienced project management, and extra costs incurred to avoid disruptions for drivers.
My friend's neighbor's house burned down a little while ago, also in Massachusetts, the land of said Green Line.
Apparently they needed to alert their neighbors (my friend included) with flyers outlining their plans, followed by some sort of public meeting, before they could begin rebuilding their home.
Imagine being homeless at the mercy of every one of your neighbors and any one of them could arbitrarily slow you down with irrelevant concerns. This kind of tedious bureaucracy is not just inefficient, but very cruel.