Why not just extend the G? It already is Queens<->Brooklyn.
Note also that there's a long history of truncating the G train [1].
I personally would love to see the Franklin Ave Shuttle extended to make a loop out of Brooklyn portion of the current G train route along Church Ave, connecting north-central Brooklyn to Williamsburg, Greenpoint, and Long Island City. That's probably a pipe dream.
[1] https://en.wikipedia.org/wiki/G_(New_York_City_Subway_servic...