This just in from Gothamist: reconfiguring the layout of subway car seats might give the cars greater effective capacity with the same number of seats. The thinking is that there are certain behaviors that lead to inefficient packing of subway cars, mainly people's desire for personal space and preference for holding on at hand level rather than holding on above head level. And I thought all those people standing in front of the door and not moving in to the car were just selfish asshats.
I'm not sure about the idea that riders who know they aren't getting off soon are any more likely to pack in to the ends of the cars - I often see people standing right in front of the door for many stops even on half-empty trains. But I do like the designs where (at least some of) the doors are staggered rather than opposite. On lines where the doors open on each side of the train at about the same number of stops, this should help move people in and away from the doors at least a little more often.
Until the science is complete and new cars are in place, just remember that blocking the door slows down the train at every stop and that's a lousy tradeoff for getting out a tiny bit faster when it's finally yours. Similar logic applies to those waiting behind the yellow line to board the train.