http://io9.gizmodo.com/unbelievable-nail-houses-around-the-w...
New subway lines in NYC can't use the latest technology. They're being integrated into an existing 112-year-old subway system with the highest station count and track mileage in the world. I'd make a software development analogy, but it would be woefully inadequate at comparing the scope of the situation.
Why are those control systems so old? Well, a 24/7 system is difficult to do maintenance on!
Digging new tunnels should mostly be independent of operations in existing tunnels.
Only in some areas, mostly in Manhattan. The outer boroughs, especially in areas where the tracks are elevated, usually only have two.
When major track work has to be done the MTA has a habit of just shutting down a line temporarily. For the past couple of years they've been shutting down the 7 train (which goes from 34th street through Times Square in Manhattan to Flushing in Queens) multiple weekends during the summer, and it has had an impact on businesses.
This argument is pure BS that tries to explain New York's incompetence when it comes to planning and building infrastrucure by citing its exceptionalism.