Part of the problem is that people at express station are not used to letting the local go by to wait for the express, as they are on long-established routes like the 7. In time, this could change, more likely so on longer lines like the 4 than on shorter lines like the W.
Another problem is that the several lines with 3rd tracks often have no express station for many stops after the terminal, resulting in the expresses being fairly empty on leaving the terminal and not filing for a while, while the local stops near the terminal get overcrowded. Ideally, the first 2 or 3 stations after the terminal should also be express stops, as on the D line. But the old elevated lines (1, 2, 4, N/W, W in Bklyn) were not built this way, for some reason.