Instead of two Bayside-Wall Street routes, maybe have one route that combines elements of the QM2 and QM20 (call it QM22?)— for example, from Bell & 212th via Bell, 23rd Avenue, Corporal Kennedy, 26th Avenue, Utopia Parkway, then follow the QM2 Saturday/Sunday routing.
As for the QM3/13, a Wall Street variant might be even more useful than the Midtown service (which duplicates the LIRR).