Perhaps it should be run the way Metro-North West of Hudson service is run; NJT would operate the service. SEPTA would contrubute money to NJT equipment purchases, and NJT and SEPTA would split operating costs appropriatly, with SEPTA completely funding trains that express between Newark and Trenton, NJT completely sponsoring trains that express 30th St. to Trenton. Locals and limiteds would be split 60% NJT, 40% Septa, based on trackage percentages. This would create a system that completely uses NJT equipment. Equipment that is fit for a hundred mile intercity run.
Most trains would follow a limited style schedule that would perhaps, besides Center City, stop at N. Philly, Holmesburg, Cornwells Heights, Trenton, Maybe Hamilton, Princeton Junction, sometimes New Brunswick, Metropark, and then the urban stops.
This fills the Clocker's shoes and then some at a price useful to Trenton Shuffle commuters. This would essentially restore the quality and affordability of NYP to Philly service under the PRR until A-Day, when AmRip prices forced the average commuter to use SEPTA subsidized commuter service, which stops in every backyard in the Delaware Valley, and NJDOT subsidized commuter service, whos only equipment that was less than half a century old was the (then) relatively small fleet of Jersey Arrows.
"The Erie only sells 1 way tickets on the NJ&NY because it only has a 99 year lease on the line."