Come on, you gotta add more information for a suggestion for a System this big. Anyways though, I want to see the Seventh Ave Line, Lexington Ave Line, or the Flushing Line.
How about IND 6th avenue line via 23rd Street 6th Avenue. I've been on that line in January 2015 and July 2017. Rolling Stock for that are R68 B & D trains R68A B train R160A-1 M train 8 Cars East New York yard BMT Eastern Division R160A-2 and R160B Alstom F train Jamaica Yard. As of right now F train has been getting R160B Siemens from Coney Island yard originally on N,Q & W trains. Also add BMT Broadway Line that includes Manhattan Bridge Dekalb Avenue.
For me it's between 6th Avenue and flushing line because you can transfer between the two at 5th Avenue Bryant Park. If you're wondering where is the transfer located actually on the Northern end of Sixth Avenue platforms lobby which actually connects to the Flushing Line lobby which is actually on top of the Island Platforms. If you own both downloadable content provided you have to an emergency scenario where you terminate a 7 train at 5th ave Bryant Park then you walk over to the Sixth Avenue platforms there's going to be a prompt for you that will say would you like to take over this Brighton Beach Bound B train yes or no? If you actually choose Yes then you load up B train 5th Avenue Bryant Park-Brighton Beach via Manhattan Bridge Northside and the Dekalb Avenue interlocking. An accompanying train announcement it's something like this ladies and gentlemen we are momentarily held by the train dispatcher due to high train traffic ahead. That will also be the problem for the 7 train provided you need to terminate at Times Square 42nd Street Port Authority Bus Terminal instead of 34th street-hudson yards.