Ideally there would just be a train every hour from Penn Station and Grand Central directly to JFK and LaGuardia but I don't see that happening in the next 20-50 years.
My understanding is that a new link to the airport was in play when they chose the 2nd Av. line. The 2nd Av. will obviously benefit many more people and is a good choise. I hope it won't take decades to sort out the airport connection. The cab ride to and from JFK is one of the most disheartening parts of living in NYC.
The real annoyance is how hard it is to get to LGA and that you're reliant on buses. It's a shame that they ran out of money building the N/R and it stops at Ditmars instead of continuing on to the airport.
I fly out of NYC biweekly, I generally fly out of JFK so I can take the E/Airtrain there (about 50 mins) and then fly back to LGA and take a towncar home, due to landing later and avoiding traffic. I'd never take a cab to JFK, it can be nearly 2 hours from midtown in traffic.