I think it's too much of an inconvenience for people to make the transfer, especially in this summer heat. I'm a regular Nostrand Avenue rider and I've never noticed the junction being that much of a bottleneck. At most it is a 2 minute wait. Arriving to the Flatbush terminal is way worse. Even if they de-line rogers, they wouldn't run enough trains to make it worthwhile, the Lexington line is already crowded enough with trains approaching every 2-3 minutes.
Bottom line is, people are selfish. If you remove a train line from them, they are bound to complain. It would never go through.