Everyone should face it. All three NYC area airports are poorly laid out.
First, I'll address the NYC airports (LGA and JFK). LGA and JFK both have horrible runway configurations. LGA could handle more traffic if it had parallel runways instead of crisscrossing runways, but that will never happen. The answer lies in JFK. JFK is, in fact, the airport that could hypothetically have its entire configuration redone. What could happen is that it could have a terminal layout similar to that of Atlanta, but maybe only three or four satellites, instead of the six at Atlanta. With the extra longitudinal room, another parallel runway to 13/31/L/R could be built, abolishing the need for 4R/22L. Then 4L/22R could stay as a reliever runway for smaller, lighter aircraft. Also, some sort of direct airport monorail or subway shuttle should be built to shuttle passengers ONLY between JFK and LGA, and then some domestic flights should be transferred from overcrowded LGA to newly efficient JFK, relieving LGA and taking advantage of new room at JFK. Also, I agree that no aircraft smaller than maybe an ARJ (69 seats with NW) should be allowed to use LGA and JFK airports. Of course this will never happen because it would cost well into the billions to do, and would cripple air capacity at JFK during reconfiguration.
Now for the answer to EWR's congestion, which is nearly the same, but with a couple of critical distances. EWR does not have the room to be reconfigured, so it will have to make do with it's current capacity. The key is in a small airport in NE New Jersey, and one that I lived rather close to for five years- Teterboro. So here's my idea. The NJ Port Authority does not like jets to operate out of Teterboro, but they could easily be pressured into allowing TEB to become a commuter port. And what carrier that we all know and *cough, cough* love operates a huge commuter operation at EWR. Continental Express. If all Continental Express flights were operated out of TEB, that would eliminate at least 150 (or more?) flights a day at EWR, lessening the chance that one would be at the end of one of those 20-plane long lines for takeoff. TEB has two runways, both over 6,000 feet long and 150 feet wide, ideal for Continental Express' fleet of ERJ's. I'm not sure if they crisscross or not, but TEB could probably handle about 40-60 operations per hour (I'm being optimistic) with decreased activity at EWR. This creates much more room for growth for Continental Express out of the NE New Jersey market and other commuter carriers would have to use the TEB airport, further relieving congestion at EWR, as well as JFK and LGA. The only missing link would be a direct shuttle link between EWR and TEB, (like the one I mentioned in the first paragraph). This would make connecting a little bit more of a headache, but one who was flying ROC-DFW on CO could fly ROC-TEB on Express, then take the train or subway or whatever to EWR, then take a CO flight to DFW out of EWR. Continental would dislike this though, because it would cost the carrier mucho dinero to shift its flight schedules to suit connections from TEB-EWR. But CO does not have to worry, because the Port Authority will not spend the billions to make this plan reality.
If something like this was to happen, NYC travelers could definently have a better travel experience, but a combination of economics, NIMBYs, and politics would doom this plan were it ever to come close to being reality.
Tell me what you think!