I don't see how you can avoid this problem without building far faster than the US currently wants to. (Largely because many argue that we don't need to build dozens and dozens of new projects simultaneously, whether subway or anything else infra-wise, all at once.)
You won't get competence in managing the budgeting, planning, and execution of a subway line without doing it a lot.
So how do you break the cycle of inefficiencies leading to people scared to start enough projects necessary to build expertise?
There's a bit in here https://chrisgagne.com/1255/mary-poppendiecks-the-tyranny-of... about how we haven't matched the construction speed of the Empire State Building since then, and a lot of it is because the depression + war that happened right after it was done cause all that knowledge to be forgotten.