If your capacity is given as 30 trains per day, it's not much of a trunk line. The existing signals in the tunnels support a rush-hour burst of 24 tph. What I'm talking about is increasing that to about 30 tph, which is feasible, and happens on the Berlin S-Bahn, Munich S-Bahn, and Paris RER, all of which are mainline systems.
There aren't enough people in Monmouth, Ocean, and the coastal parts of Middlesex working in New York and Newark to put 90,000-120,000 daily riders on a line. If everyone who currently takes the NEC and the North Jersey Coast Line switched then sure, but then what's the point? Direct train service to Toms River has some benefits, but they're far down the line.
It is just not true that the alternative to ticket punchers is faregates. New Jersey isn't Tokyo and never will be; Swiss or German POP is going to work just fine for its rail ridership. Of course NJT does the worst of both worlds, with the internal faregates at Secaucus and the constrained vertical circulation... even the LIRR, not normally a very competent organization, does this better, with timed cross-platform transfers at Jamaica.
Most reorganizations that Americans think are impossible or very difficult or will take a long time are actually easy when done by people who know what they're doing. SEPTA was going to complete them very quickly, until the workers rebelled (who are those
stupid European immigrants to tell us how to run a railroad? What was good for my grandfather is good for me!).
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