Considering Kings Plaza is on Flatbush Ave, let the T go to Ozone Park (eliminate two A branch trains) and instead extend the 2 under Flatbush Ave and extend the 4 under Utica Ave to meet at Kings Plaza (Utica & Flatbush meet only a few block away).
I am tossed up about the Y. While useful, lots have been spent improving (height clearances) the Bay Ridge for freight which would all be wasted if turned into subway. Personally, I would like to see the Bay Ridge Branch reused by LIRR operating between LIC, Queens to NY Container Terminal, SI via rehabed SI N.Shore RR and tunnel between 65th St Yard Brooklyn and St.George SI. The tunnel should be 2 level, similar to 63rd street tunnel built for ESA, so one level can be given to Subway to connect to rest of the city's subway system (become the U on this map). Break fares down to SI and Brooklyn/Queens, so if traveling within the same zone (ex: NYCT to St.George) on this LIRR line, charge the same as subway, but more typical LIRR rates if crossing zones. In SI: rehab all the SI N.Shore RR stations. In Brooklyn: rehab ENY lower station for interconnection to Atlantic Branch & subways and add the New Utrecht Ave & Brooklyn College/Flatbush Ave for more interconnections between subways. Not sure where to best put stations in Queens. The idea of going to Queens from SI is the hope that a new tunnel will be built to NYP under E.River from LIC or build a new tunnel to connect Lower Montauk to ESA at Sunnyside, in either case the idea is to allow ride from NYP/GCT to NYCT. If to NYP, NJT might be interest in using this route.
As for the rest of the Y between Flushing thru The Bronx to 190St/Ft Wash Ave , maybe the 7 line could be extended for that purpose.
Another extension that might be interesting would be for the N train to continue past Ditmars Blvd over the Con Ed property then turn east and run underground to LaGuardia Airport.