JFK is one of 3 Major Airports within a 25 mile radius, there are at least 3 more smaller airports within 50 miles, and they all need airspace. When the weather is clear, the airspace around New York is packed to capacity most of the time, when the weather deteriorates such that full Instrument Flying clearances are required, there isn't enough airspace so flights get held or stacked. So before you even look at the effectiveness of JFK as an airport, the airspace is simply too busy to allow effective operations.

Then you are mixing domestic connections with international flights, always a recipe for delay and confusion as there is so much scope for late arriving flights. Depending on the wind direction, JFK uses variations on its pair of parallel operating runways for t/o and landings, but the runway pairs intersect at 90 degrees, that's quite common, but it limits traffic flow. Atlanta has 2 pairs and an additional southern runway, but all parallel to each other so they can use all 5 simultaneously.

Then there are the delightful RJ's. An RJ takes as much airspace, runway, taxy time, jetway and ATC to get 50 people in and out as a 747 takes to get 350 people in and out. Now you need RJ's at some point, but in terms of their impact to a major international hub there is an obvious load factor penalty.

Hey, 3 paragraphs of woe and we haven't even started bashing Delta yet!

Delta's decision to make JFK a major hub is not rocket science - it's where a lot of customers live and where international visitors want to fly to. Telling most of your international customer base they can't fly to JFK because it's a terrible location for an airport is not really good business. So instead they are forced to deal with high volumes of air traffic at an airport that passed its best-before date in about 1974. If everyone wanted to fly in and out of Cincinnati it would make a fantastic International hub - but they didn't and they don't.

So the very long answer to your post is you need to make some assumptions before you ever book a JFK flight and manage those expectations accordingly.

1. Expect late or missing connections because of the ATC SNAFU's so try to travel early in the day (less chance of delays at 06:00) or make sure you have a good book.

2. If you notice the weather is poor ANYWHERE in that North East sector then expect delays (see point 1).

3. Don't expect the GA's to know much more than you do - the ATC slot lottery can be won at anytime by a low-fuel international inbound, pushing your BUF connector to the back of a long line.

4. Don't expect it to get any better unless somebody reinvents the laws of physics around airspace usage or closes EWR and LGA.

Sadly the bottom line is JFK is a carefully designed and constructed passenger nightmare that can't be fixed, so there's little point in letting it wind you up.