Another thing that is a factor in their decisions is a constant push to remove the "Jamaica crawl". This effort is not so much to punish the Brooklyn customers, but an effort to remove the switches involved. If you have lots of switches, you can't have "code" permitting faster movement. Especially now with this PTC behemoth dumped on the railroad. This is something they've been banging their heads against for a long, long time. Management going to Signal and asking how do we pump up the MAS? The answer is simple, reduce the amount of turn-outs, etc. But to do that then you have to take away your ability to make complex moves, primarily across Hall as mentioned by K&K. Another thing to reduce the crawl is to eliminate connections. Often the RR must hold a connection so the Brooklyn trains can match up with their connections. Move the Brooklyn operation out of the main flow of traffic, eliminate the connections, and just pump the other trains through, drop and go. Less delays, higher OTP, and LESS CRAWL.
Does it work for everyone? Probably not, but they're aiming at what's been a goal for decades, faster rides for the majority trying to get into Manhattan.