As a New Yorker, I much prefer LaGuardia, and strongly disagree with calls for its closing.
The point is, I think, that in exchange for an improvement (real or hypothetical) in convenience for a small fraction of total air travellers, there is a substantial and arguably unnecessary burden of cost and inconvenience to the entire system (which is ultimately paid for out of everyone's pockets--and user experiences).
I would love to see these large airports replaced with multiple smaller airports. A larger percentage of the population would have an airport nearby, and average travel times would be reduced significantly.
Well no, it wouldn't. A fully-served point-to-point network with n nodes (cities served) has on the order of n squared links between nodes. The number of passengers desiring each direct link gets to be very small, very quick, meaning infrequent scheduled flights on small, underfilled, costly-per-seat aircraft. So what happens is that airlines adopt (to one extent or another) a hub-and-spoke model. Most direct point-to-point routings are dropped. If I want to fly from East Podunk, NY (POD) to Los Angeles, I can't get a direct flight POD-LAX. Instead, I get a hop to an airline's hub (JFK or ORD or DTW or wherever), and a connection from that hub to LA: POD-JFK-LAX, or POD-DTW-LAX, or POD-ORD-LAX.
If I want to go to a destination served by a smaller airport (let's call it West Lemon, CA: LEM), then I'm taking three flights: spoke to hub, hub to hub, hub to spoke: POD-JFK-LAX-LEM. And each of those flights carries with it the time penalties associated with loading and unloading passengers and cargo, and a risk of delays or cancellations due to weather and other circumstances--plus the plain old waiting for connections, because service to and from the small airports at POD and LEM is infrequent.
Worse still, all those little commuter flights linking the regional airports to the major hubs are going to take up gates and takeoff and landing slots at those busy airports, slowing down the whole system and/or pushing those less-important flights to less-desirable times of day. Taken all together, offering frequent (or even just daily) service to a lot of small airports is going to mean a lot more flights of a lot more smaller aircraft, and/or passengers frequently making multiple connections. It would be expensive per-seat and vulnerable to failures and delays.
Now, La Guardia is an interesting case. Since it's right next to downtown New York, it draws a substantial number of departing or arriving passengers, and enjoys a kind-of-weird pseudo-hub status for historical reasons. Practically speaking, though, it means that there are effectively two hubs (LGA and JFK) or even three (if we count EWR) serving the same area, resulting in needless duplication of services. Routes that could enjoy frequent service with inexpensive (per-seat) full-sized jets get less-full or more-expensive aircraft, or less-frequent services divided between two or three New York destinations. Local New Yorkers enjoy the appearance of convenient, direct flights, at the cost of making the rest of the system a bit worse and a bit more expensive for everyone.