The reason of the difference I think is the method of building tunnels. The NYC subway system is build long time ago, when cut and cover is acceptable. The width of the tunnel thus can be very wide, especially considering cost. Make the tunnel twice as wide may only cost less than 50% more (I'm guessing the number). Modern tunnels are mostly built using TBM, in which case the cost of making the tunnel twice wider may cost more than 100% because of the affects of multiple TBM working side by side may be hard to predict and hard to coordinate. So in this case it may be better to just build a regular line first, and than build a express line in a different route.
I'm not a civil engineer, so my reasoning may be completely wrong.