Bro, I'm going to blow your mind right now. Ready. Look at the map and read the names out in alphabetical order. What do you find?

(123456) - The Bronx
(ABCD) - Also the Bronx (or close)
(EFG(H?)) - Queens Blvd (note the G no longer goes past Court Sq).
I is skipped because it looks like 1.
(J(K?)LM) - Bushwick and Williamsburg straight to Broadway Junction (skipping Downtown BK). Runs parallel to EFGH but further South.
O is skipped because it looks like 0.
(N(P?)QR) - Coney Island (usually) to around 50th st then (usually) turns off to Queens.
S always denotes a shuttle.

oh and the 7 goes to Flushing and W/Z exist but they break the pattern. W should be P, Z should be K, arguably R should be H and Q should be T. Done. Thats the whole system.