@Bracdude, NJT did comprehensive studies to determine the biggest interest by passengers with least environmental impact and determined it would be the Jamesburg NEC routing.
Freehold to Matawan required too much reconstruction and just dumped everyone back on the Coastline and more importantly, ran directly through the backyard of some very well off and influential people (much more so than Jamesburg/Monroe.
Farmingdale to Red Bank did not provide enough adequate passenger traffic expansion for the expense and just dumped people back on the Coastline as well.
I am not sure if the MOM thru Jamesburg was going to be considered a serious commuter route for NYC bound passengers, but it did provide a healthy connection to New Brunswick. And depending on how they built the connection with the NEC, if they used a transfer station, it would also provide a healthy connection to Trenton & points south.
The main problem with all routes was availability of slots on the NEC for more trains. The multilevel cars were introduced to ease the traffic burden and the new tunnels will help with also. But as to running on the NEC in general, it is a very busy railroad as it now stands. that's why a transfer station somewhere around Monmouth Junction could be ideal (be similar to Long Branch).