Here is a proposal I am thinking of, perhaps it would be a long-term goal for NYC to consider.

Once the ARC, ESA, New Lower Manhattan East River Tunnel are someday complete, the following would be a logical next step:

Bore a new deep tunnel from lower manhattan to midtown for commuter rail rapid transit able to accomidate all the different power sources used by MN/LIRR/NJT.

Such a line would connect to the Calatrava hub and the new tunnel to Brooklyn and on the other end would connect the ARC tunnels near PENN and to Grand Central's MN tracks.

Stops would include major transit nodes such as Union Square, Penn Station, Times Square, 5th avenue/midown and finally grand central.

The following could take place:

1) Access from NJ suburbs directly into Lower Manhattan and on to Brooklyn. Newark airport to Lower Manhattan and GC.

2) Acces from Brooklyn/JFK airport directly into NJ

3) Easy Access from CT/Westchester to LM and Brooklkyn without a transfer.

4) Access from any suruban area to anyother without transfers.

Best of ALL --> Quick access from EWR to JFK without a transfer would be possible -- or one transfer at Jamaica.

It would be accomplished by the creation of a new branded train system that would make tru runs from i.e, LI to NJ, CT to LI, NJ to CT, etc.... via the trunk line in manhatan.

There you have it, one tunnel could link up 3 transit networks, allow for trips from the airports to various parts of manhattan. A true regional system. A large sum of money, but what an investment. Kills the 2nd avenue subway for value. Manhattan really needs a trunk line connector, it would take a load of the subway system and allow for intra-manhattan exress trips also.