I'm batting around a plan, without an eye to cost, for using bits of commuter rail to run new 2nd Av services:
(As I am graphically challenged, forgive the amateur hour visual accompaniment)
: Coney Island to Wakefield (or Mt Vernon) via the Metro-North Harlem Line
: Kings Plaza to 125th & Broadway (or just Park) via Utica Ave & the LIRR Atlantic Branch
New, blue, : Valley Stream to Bayside (or wherever) via Northern Blvd & the LIRR Port Washington Branch
I see a number of issues with this like getting from Hanover Sq to Atlantic Terminal (I'd like to send the T & V through the Montague Tunnel but there'd be a whole mess of capacity constraints to that) & that these are pretty long routes (which could be mitigated by keeping Nostrand Ave as the only intermediate stop between Atlantic-Barclays & East New York) but it'd be adding service to some of the densest areas not served by the subway as well as new trains to far eastern Queens.