If I had my own fantasy subway routes, I would create the following:
(1)/(9): Similar to original skip stop service but the 9 runs express peak direction between 96 Street and 145 Street. (145 street would be converted to a 2 track 2 platform station so uptown 9 trains don't skip 145 Street.) The 1 and 9 (vice peak direction) would stop at all stations south of 168 Street, with the 1 stopping at 181 Street, Dyckman Street, 207 Street, 225 Street, and 231 Street and the 9 stopping at 191 Street, 207 Street, 215 Street, 231 Street, and 238 Street.
: Rush Hour service to Nereid Avenue would run express south of Gun Hill Road.
(8): Lexington Avenue Local Service running between Brooklyn Bridge and Gun Hill Road, making all 6 stops in Manhattan and all of the 3 Avenue El stops in The Bronx, plus new stops at 143 Street (Willis Avenue), Willis Avenue- 138 Street, and 3 Avenue - Bruckner Boulevard between 149 Street and 125 Street.
(A)/©: The C extends to Lefferts Boulevard and all A service ends in the rockaways; the late night Lefferts shuttle is renamed the C
: Service runs to Bedford Park Boulevard at all times, or at least whenever it operates.
(J)/(Z): Similar to my 1/9 proposal, the J would make all stops west of Broadway Junction with the Z making express stops west of Broadway Junction.
: Back to its 1980 days on 8 Avenue, the K runs between 168 Street on the A/C lines and Hings Highway on the F line. This would be a weekday only route and makes express stops between 145 Street and Church Avenue. The reason The K makes stops north of 145 Street is to reach the same terminal tracks that are in use on the C train.
: Its current 2 Avenue line proposal except it ends on Broadway and 125 Street.
: The T would be almost different from what it is proposed now:
It would run between Throgs Neck - Harding Avenue and Rockaway Park (Replacing The Rockaway Park shuttle), Running as the Throgs Neck Local, 2 Avenue Express, Fulton Street Local, and Rockaway local. Late nights, all stops are made.
(U): This route would combine 2 things, the current proposed T route north of Grand Street and the original M route south of Chambers Street. The route would use the original Nassau Street line's Manhattan Bridge tracks to connect the 2 Avenue and Nassau Street lines. Late nights, no service. (Maybe the Nassau Street line could be converted to allow the R68 D trains to run on the U between Grand Street and Dekalb Avenue)
(Y): A 2 avenue subway weekday route running between Hanover Square and Jamaica - 179 Street via 2 Avenue local, 63 street local, and Queens Boulevard Express. The Y make ALL express stops on the Queens Boulevard line.