I think once ESA and the 3rd tracks are complete, LIRR really needs to redesign its service.
Have most of the electric service run to GCT and FBA, and have it mostly DM at NYP. Have a few new services. The Port Jeff and Montauk lines could really be revamped. 3 levels of service for the PJ. Maybe something electric from Huntington making every stop to FBA. From PJ, express making all stops to Huntington, Syoseet, Hicksville, Mineola, Floral Park, Jamaica, Sunnyside, NYP......and a superexpress PJ-Stony Brook-Smithtown-Huntington-Hicksville-Mineola-Jamaica-Sunnyside-NYP
The Montauk line could start service on the main line. Maybe something from PD making all stops to Babylon, re-open south Farmingdale, then on to Hicksville, Mineola, Jamaica, Sunnyside, NYP. From Montauk, have 2 levels of service, express and super express.
Montauk-Southampton-Westhampton-PD-Bay Shore-Babylon-Freeport-Jamaica-NYP
All stops to PD, Bay Shore, Babylon, then 1/2 running Hicksville, Mineola, Jamaica, NYP, and the other 1/2 running Freeport, Jamaica, NYP
Boost Greenport service. Have them run all stops to KO, Brentwood, Wyandanch, some Farmingdale, Hicksville, Mineola, Jamaica, some Sunnyside, NYP
Maybe express service running Greenport-Riverhead-Yaphank-KO-Hicksville-Mineola-Jamaica-NYP
From KO, run all stops to Hicksville, Mineola, Floral Park Jamaica, and then half to GCT stopping at Woodside, and half to FBA making all stops.
Babylon should probably stay mostly NYP service. Have express and local. Express running Babylon-Amityville-Massapequa-Freeport-Rockville Centre-Lynbrook-Valley Stream-Jamaica-Sunnyside-NYP
The locals could run all stops to Valley Stream, then Jamaica, Sunnyside, NYP.
The 3 lower nassau lines(WH, LB, and Far Rock) could be split into 1/3rds. 1/3rd of the trains to GCT, 1/3rd to NYP, and 1/3rd to FBA. At no time should 2 trains from any of those 3 lines be going to the same destination. Probably run these lines at 20 min intervals peak, 1hr off peak weekdays, and 40 min weekends. Have express and local. Locals would make all stops to the destination. Express would run to Jamaica, and then on NYP trains, they'd stop at Sunnyside and NYP, and on GCT trains, they'd stop at Woodside. Also, express trains would run non-stop from Valley Stream to Jamaica(meaning Locust Manor, Laurelton, and St Albans are local only).
Hempstead line.........uhhhhh. Maybe have it run 1/2 NYP, 1/2 Hunterspoint. Maybe have them make all stops to NYP and Hunterspoint.
PW line can run 1/2 NYP, 1/2 GCT. NYP express makes stops at Flushing and Sunnyside, and GCT express makes stops at Flushing and MAYBE Woodside.
OB line, boost service and run half to NYP and half to LIC. Half the LIC via lower montauk(re-open all stops), and half the LIC via Hunterspoint.