First off, "express" does not necessarily mean "faster". Second, if you think the crowds in Brooklyn are bad, try a train that trudged through everything north of 59th Street, only to have to pick up a bunch of people in Midtown while dropping loads of others off. Combined with the concept of proximity (hell, Brooklyn has more options in one place than Midtown), it's very easy for people to get to their destinations in approximately the same amount of time from Brooklyn as it would from Midtown (GCM's depth is especially glaring in this regard).
I didn't mention this earlier, but for some who may use Atlantic Terminal (albeit a minority), it would cost significantly less than to go through Penn Station while requiring far less time on average than using a bus + subway itinerary.