You kind of point to the reason why its so expensive to build in the US: we stopped building. Any new projects are unique which requires special orders on everything. When you're constantly building and upgrading, your overall costs keep dropping.
There’s that but there is also a lot being spent on the wrong projects. East Side Access has not really moved the needle on ridership, which is a very big contrast compared to say Crossrail in London which was built in the same time frame.
There's also a lot being spent on things that are not even transit, but are required/customary of transit projects. The consultant-class has to get their 10 pounds of flesh, and every project is needled to death by outreach, impact studies, environmental reviews, delays, more environmental reviews, etc. We pay a lot more for the stuff, sure, but we've already blown half the spend before we've even started the job of putting stuff together.
This is of course an over-correction to an equally bad world where you can just get some dopes together to slice up your city like a Christmas ham, usually by demolishing the poor and non-white parts, to build highways.
