It was the Air Transport Association on behalf of the airlines which sued the FAA, in 2008. The FAA sought to control peak time landing and take off slots at Liberty, LaGuardia and JFK by auctionng slot pairs. Their motive was to reduce congestion and eliminate "structural" delays of the sort the OP complains of at Atlanta. The FAA argued that slots were property, controlled by the FAA. The ATA argued that the FAA was exceeding its powers and that airlines were free to set their own schedules and that this was a breach of their rights to do so. I think it was ultimately settled, but not entirely sure of the outcome. My point was that it is the airlines who control volumes at peak time "pinch points" not the FAA, and they have resisted attempts to address this problem.
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