I just had this weird (yes, I know that this will sound really weird and probably ridiculous) idea for a new in a similar alignment to the proposal... but with a slight twist.
A new connector near Bowery/Grand Street would have to be put into place in order for this to work, or you could be ridiculous and reverse the train at Essex. Anyway, here is my weird plan (probably very limited rush hour service only):
Orange \ Sea Beach Express \ 4th Avenue Local \ Nassau \ Sixth Avenue Local \ Second Avenue
Coney Island
Kings Highway
(Option to go local or express to 59th Street after)
59th Street All 4th Avenue Local stops to DeKalb, then continuing via the Montague Tunnel to the Nassau line:
Broad Street All Nassau stops to Chambers or Canal Streets. If to Chambers, then a connection can be made to Grand Street , or of to Canal, then an additional connector before Bowery would have to be made. If both options unavailable, then the train proceeds to Essex Street and then reverses to the Sixth Avenue Line. All 6th Avenue local stops are made to Lex-63rd, then via the Second Avenue Line to:
96th Street