With that being said, they could at least modernize the Port Jefferson Branch by rehabilitating stations to match their neighbors.
-St. James, Smithtown, and Greenlawn.
-Add a second track/platform at Northport (there's room)
-Bring double-track service to Greenlawn if they enhance the station. There is a Platform B.
As far as the Central Branch, I would say just electrify it simply. Make it an express track/route with no stations from Belmont Junction at Babylon to Bethpage.
This station is Babylon, this is the train to Penn Station. Stopping at: Lindenhurst, Copiague, Amityville, Massapequa Park, Massapequa, Seaford, Wantagh, Bellmore, Merrick, Freeport, Baldwin, Rockville Centre, Lynbrook, Valley Stream, Jamaica, Kew Gardens, Forest Hills, Woodside, Penn Station.