That sounds terrible. Unfortunately it seems par for the course with many airlines based on other reports like this that pop up from time to time. If it were me I would have called AA as soon as I knew I was heading back to JFK and gotten rebooked some way some how on another flight, even if it meant connecting, to avoid being in the same situation as hundreds of other people, as you experienced. Obviously that isn't always practicable with bags, etc., nor is it "fair" in every sense (those with status and familiarity with airline rebooking, lounges, etc., will get better results), but I sure as heck wouldn't stand in any line for 3 hours unless it was a line for water and I was about to die of dehydration.