Here are my ideas.
IDEAS THAT DON'T INVOLVE NEW TRACK:
Send the to Lefferts Blvd to replace the . Late Nights service would be cut back west of Euclid Avenue, eliminating the need for the .
Since service only runs in the peak direction, take advantage of this and use the entire express track from Ave X to Jay St.
Swap the and routes between 47-50th Sts and 36th St. This would eliminate the switching tracks near Queens Plaza, and the switching tracks south of 36th St.
service should just be replaced with a , that would run peak direction express between Broadway Junction and Marcy Ave, stopping only at Myrtle Ave.
Run like the , as a weekday peak direction express, not just rush hours.
Just rename the to the . It would make the system so much simpler.
Swap and routes in Brooklyn, with rush hour express service to/from Bay Parkway.
Do something with the and at 75th Ave and Briarwood, either only stop one of them, or stop both of them, because the situation right now is too confusing.
IDEAS THAT INVOLVE SOME NEW TRACK
Build switches at Hoyt-Schermerhorn Sts, connecting the and , to enable a connection between the lines for train movements, and to be used during service changes.
New Switches just east of 7th Ave - 53rd St, allowing a connection for a Bronx-Manhattan-Queens Line.
IDEAS THAT INVOLVE A LOT OF NEW TRACK
New line using the tail tracks beyond 2nd Ave station, would provide a new East-West line across Queens. Possible route could head along Houston St before heading under the East River, with a Connection to the and at Lorimer-Metropolitan, and another connection to the at Montrose Ave, and a connection to the either at Wyckoffs Av or Knickerbocker, before tying into the Jamaica Line at Cypress Hills. Note this route was planned using a track map, not a street map. Line may be designated .
Obviously the completion of the , possibly with an extension into Brookyln.
Extension of the to Bedford-Nostrand Avs, preferrably with some sort of track connection to the , as well as the double tracking of the entire line, to allow for a new line to Brighton Beach or Coney Island from Court Sq, most likely would remain as a shuttle during late nights.