I think the issue is that to bring the new line to the same grade as the existing terminal would have required some other exceedingly expensive tunnel so the trains could wind their way up to the correct elevation. This is the same reason that the F train, which uses the same tunnel, has such deep stations under midtown east

yes, just want to add that a huge reason the neighborhood is so nasty is because its covered in vornado sidewalk sheds, dirty sidewalks they are responsible for cleaning, and empty vornado realestate