Hello, this is a video by RMTransit about a cool proposal by the Effective Transit Alliance. It’s about a through-running regional rail system. Here’s the link from the description to the entire proposal: https://www.etany.org/modernizing-new-york-commuter-rail
This project would be amazing, if it could be done. I don’t trust NYC to get this project done as-is, it’s just too corrupt. You need an institutional change to make this even possible. The other huge challenge here is the bottleneck that is the Hudson Tunnels. The current tunnels only allow 24 trains per hour each way, including regional, commuter, and long distance trains. It’s difficult to imagine high frequency commuter service without cutting Amtrak service back. Crash-worthiness would be an issue too. You would be mixing brand new trains with Amfleet rolling stock that is coming up on 50 years old, and crashworthy standards vs performance would be an issue. The way to solve this is of course the Hudson Tubes project and connecting Grand Central to Penn Station is obviously a great idea, but you are still losing capacity even with 2 tunnels because of the old tubes. The way to do this properly is even more expensive, but it would be worth it: 6 tracks under the Hudson. The oldest tunnel set for regional and long distance trains, the new project for the Penn to Grand Central line, and yet another tunnel for the New Jersey - Long Island line. This would allow for proper metro frequencies on the core line segments, and would be a very expensive project that would be absolutely worth it long term.
In terms of how incompetent NYC is right now, not only is the East Side Access project a huge boondoggle with little benefit in terms of capacity, the part of the line it does free up (service from Jamaica to Atlantic Terminal) is managed very poorly. You should be seeing bare minimum a train every 10 minutes between these two stations, but the MTA can only manage every 20. It’s so bad that iirc they had to partially reimplement the old schedules after riders kept rightfully complaining about missed transfers at Jamaica.