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
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.