So far, here is a map, I mostly revived the subway lines and altered some existing lines into my proposed line, to gain convenience and service flow rates to the MTA Customers.
will take over the 125 Street Harlem Crosstown line, left into The Bronx, the one that will be constructed in the future. Then it will ply on the 
line from East 180 Street to East Dyre Av, then it will operate via the 
in the Bronx. Also, 
will be revived to takeover the uptown Manhattan line, plus it will be extended to Riverdale 263 St. Furthermore, when gets to midtown, it will run express in both directions during rush hours from and to Coney Island, and in the regular hours, this train will terminate at World Trade Center with the 
. So, 
will extend to Inwood - 207 Street from 168 St to load more customers.
At Brooklyn, won't terminate at Leffert Blvd, only stops at its home, The Rockaways. The customer who takes this train to Howard Beach JFK station, won't be confused that they might miss the Rockaway line to the JFK, thus missing their plane schedules. Instead, the will help the as its buddy to get to the Leffert Blvd, while this train operates to and from Far Rockaway.
trains are being routed back to the existing route, from 47-50 Streets Rockefeller Center to 145 St or Bedford Park Blvd, since many of the MTA forum users agreed that this line cannot go to queens at all, or their job will be more difficult.
Trains will be extended to 34 Street and 1 Avenue via crosstown line.
Trains will operate on the Second Avenue Subway line after a whole construction is finished. Meanwhile, the 
train will follow the and 
as well to East Dyre Av.
The train will operate express in Brooklyn to Coney Island - Stillwell Avenue, and will operate local to Brighton Beach. On weekends, the will operate local since they were no trains operating on all its stops.
will be revived to take over the Queens Blvd line, and will extend to Jamaica - 179 Street during peak hours, and finishes at Lower East Side - 2 Av.
Regular hours, trains operate from Forest Hills.
Rush hours, any trains that comes from and goes to Jamaica -179 Street, approaches on the express track at Forest Hills, and will service express between Queensplaza and Forest Hills.
will also come back to life, and operates between Astoria - Ditmars Blvd and Whitehalls, during peak hours,will extend to Bay Ridge - 95 St, and will operate express between Bay Ridge - 95 St and Atlantic Barclays Center.
(X) line is added and will operate between Pelham Bay Park and Brooklyn - Borough Hall. During AM peak hours, Borough Hall bound will skip Classon Av, and PM, only the Bronx bound will.
The and line designs are not my ideas. I looked up on the Google image, and searched "Rethink NYC Subway". I drew on the NYC Subway Map above.
Cited From Venturi, Jim. Rethink NYC Subway. Digital image.Http://static1.squarespace.com/static/545bfd33e4b0bb07afbc3c81/t/553f8095e4b00df897fed1e4/1430225077590/WEBSITE3.014.jpg?format=750w. N.p., n.d. Web. 4 Feb. 2016. <http://www.rethinknyc.com/newsubway/>.