My gripe with Airtrain is the same as Analise: this thing does not go into Manhattan. It was well known by all involved that if a train is not a "one-seat" option, people choose other transportation methods. I have no idea why they even bothered with the Airtrain.

What should be done is an extension of the A train directly into the terminals. And like in the 1980s, a truly 'express'
A train that makes only a couple of stops between downtown Manhattan and JFK. I am certain this could have been accomplished for $2 billion, including express tubes around the current A local stops. Then the city could run that train every 5 minutes during the day: it would enhance service on the A line and would provide a 30-minute link for the entire island of Manhattan to JFK.

(It has taken me up to 1.5 hours on the A train from Midtown to terminal check-in with the old bus service from Howard Beach).