A Sunnyside station is useless for Amtrak. It could have some utility to LIRR and Metro-North, but Amtrak will not gain much from it. If our hypothetical passenger is getting to Sunnyside via LIRR or Metro-North before boarding the Amtrak train to Boston or DC, he could have very well taken the same LIRR or Metro-North train to Penn and boarded Amtrak there. The likely time savings are small enough that there is not much difference between the total number of passengers who would be willing to take the extra time and go to Penn vs the total number of passengers who could do the transfer at Sunnyside. The other alternative for the passenger is to drive to Sunnyside, to walk or to take the subway to there. There are not enough passengers to justify this for an Amtrak stop. Why would someone from Long Island fight the traffic to just part at Sunnyside? A few will, most won't. Why would someone be willing to take the subway to Sunnyside, but not to Penn? From most locations the difference in time is minor. So you really lose only the people who would walk to Sunnyside. Even with all the condos and other stuff going on in Long Island City that just is not enough passengers to justify it.
Secaucus is a different story. Not stopping a couple of regionals there is idiotic. Nobody in their right mind will take a NJ transit train on say the Bergen Line to Secaucus to take another NJ transit train to Newark to get onto an Amtrak train to DC. Do you know what people hate more than switching trains? Switching trains two times. Yes, the Bergen County person can drive to Newark and park there, and I am sure that some do, but getting to Newark and parking there just is not all that convenient that most people would do it. On top of that there are generations of adults who were taught to never go into Newark and would never go there regardless. Some actually drive down to Metropark for this exact reason, but going to Metropark is not really convenient if your destination is the other way, say Boston. Secaucus also has the space for parking garages to be build and is conveniently on the highway, so in this way it is very similar to Metropark. I am certainly not implying that Amtrak needs to stop every train at Secaucus, but stopping a couple the way it is done for Princeton Junction is likely to get them some more passengers that they are currently missing upon. Bergen County plus Orange and Rockland in NY is quite large in terms of population and there is ridership to be had there as I know nobody in these places that likes to go to NYP, LGA or JFK to catch a train or a plane if they can avoid it. Also anyone claiming that stopping more trains at Secaucus cannot be done because it would reduce the total number of trains between NYP and Newark Penn needs to be reminded that the current bottleneck is the tunnels, not Secaucus Station which has 4 tracks. Indeed currently it is very easy to observe delays at Secaucus because the trains that stop there need to wait for the ones that do not stop to pass. The current schedule interleaving Secaucus stopping trains with Amtrak and NJT expresses is terrible for avoiding delays as it assumes very careful interleaving of the trains which probably has never occurred as planned over the course of any consecutive 24 hours.
Secaucus is a different story. Not stopping a couple of regionals there is idiotic. Nobody in their right mind will take a NJ transit train on say the Bergen Line to Secaucus to take another NJ transit train to Newark to get onto an Amtrak train to DC. Do you know what people hate more than switching trains? Switching trains two times. Yes, the Bergen County person can drive to Newark and park there, and I am sure that some do, but getting to Newark and parking there just is not all that convenient that most people would do it. On top of that there are generations of adults who were taught to never go into Newark and would never go there regardless. Some actually drive down to Metropark for this exact reason, but going to Metropark is not really convenient if your destination is the other way, say Boston. Secaucus also has the space for parking garages to be build and is conveniently on the highway, so in this way it is very similar to Metropark. I am certainly not implying that Amtrak needs to stop every train at Secaucus, but stopping a couple the way it is done for Princeton Junction is likely to get them some more passengers that they are currently missing upon. Bergen County plus Orange and Rockland in NY is quite large in terms of population and there is ridership to be had there as I know nobody in these places that likes to go to NYP, LGA or JFK to catch a train or a plane if they can avoid it. Also anyone claiming that stopping more trains at Secaucus cannot be done because it would reduce the total number of trains between NYP and Newark Penn needs to be reminded that the current bottleneck is the tunnels, not Secaucus Station which has 4 tracks. Indeed currently it is very easy to observe delays at Secaucus because the trains that stop there need to wait for the ones that do not stop to pass. The current schedule interleaving Secaucus stopping trains with Amtrak and NJT expresses is terrible for avoiding delays as it assumes very careful interleaving of the trains which probably has never occurred as planned over the course of any consecutive 24 hours.