The real problem is capacity. NYP can't handle what they're putting in there now. The tunnels aren't the only choke points--so are the platform tracks. NJT has substantially increased its frequencies and is looking at a new trans-Hudson tunnel as well as new platforms, and LIRR is so tight on capacity they're underway with a plan to access GCT with a completely new set of tunnels and underground terminal oriented at right angles to GCT's tracks. This, BTW, gets badly needed service into midtown from the LIRR.
For example, see the following links:
(NJT):
http://www.accesstotheregionscore.com/News&Events.html#Article6
(MTA-LIRR):
http://www.mta.info/capconstr/esas/index.html