Here's draft 1 of my fantasy subway map. It was inspired by the grandiose plans for the second system. I have not gotten to adding route labels, some stations, nor any station names yet, but you could probably tell by the colors.
The and the have switched roles, but the 5 will remain express and between Gun Hill Road and Third Avenue.
The is shown on this map.
The Second Avenue line is added. It has connections to the 63 Street, Huston Street, 6 Avenue, and Fulton Street lines.
The Flushing line is extended westward.
The 63 Street line connects to a new super express line that runs from 21 Street–Queens Bridge to Kew Gardens–Union Turnpike. The super express line has only one track. It also has a connection to the Rockaway line; where they run side-by-side the tunnel has three tracks with track connections right before two of the tracks veer off to the LIRR Rockaway branch.
The Rockaway line runs using the old LIRR right-of-way with stations at 63 Drive, Metropolitan Avenue, Myrtle Avenue, Jamaica Avenue, Atlantic Avenue, 101 Avenue, Aqueduct, and beyond.
The Hillside Avenue line is extended with extensions of the local services as well (which use the 4 relay tracks north of 179 Street).
The Archer Avenue line is extended. The two levels still have no connection to each other.
The Libery Avenue line is extended to Springfield Boulevard. Stations have yet to be determined.
An express track is added between Broadway Junction and Cypress Hills on the Jamaica line.
The Huston Street line branching off the 6 Avenue line is connected through the river to the Broadway station on the Crosstown line.
The Myrtle Avenue line no longer connects to the Jamaica line at grade. The tracks fly over.
The Fulton Street line branches off into another line running under North Conduit Avenue to 114 Street. The line is also connected to the Rockaway line.
The Nostrand Avenue line is extended to Avenue S. Stations have yet to be determined.
The Culver express makes its return. Locals terminate at Kings Highway.
The Sea Beach express makes its return. There are only 4 runs per day, however.
Please list suggestions! I am not entirely sure what direction to take this map.