[Busy Bee]

Its all about construction method. If you're building using cut and cover like the full length IND mezzanines, the larger stations are more affordable as you already have the street dug up and you are essentially constructing a two-story concrete structure instead of a one story structure. This becomes exponentially more costly with TBM construction since an enormous cavern is required to be mined and a much more complicated concrete structure fabricated all without access for heavy machinery from the street, long diagonal egress tunnels, the list goes on and on. And aside from the station size dynamic, tunnel boring also limits what kind of operational design is possible (or ideal) vis a vis flying junctions, 4-track cross platform stations, multiple dip-unders and fly-overs like we saw in the early 20th century because you are confined to the profile of the TBM, unless of course you want to do even more wildly expensive mining through bedrock beyond just the station caverns. To summerize, the MTA has to get back to cut and cover. A 21st century hybrid version like what LA is doing where the tunnels are bored but the station boxes are excavated and constructed while disturbing the surface street as little as possible by using temporary steel bridgework and lane diversions.