Worth your time. Good discussion in the comments section too. I've been an advocate for through-running and greater coordination among METRO-North, LIRR, and NJTransit for years now.
It won't be free, and the logistical changes will take time, but the service and capacity improvements would be worth it. We shouldn't let artifacts of the past, or the arbitrary legacy of political borders between states stand in the way of sensible regional transportation management.