Even in DC, there is a lot of public transit not managed by WMATA. While WMATA runs the MetroBus system, each jurisdiction also has its own bus system beyond that, in part because none of the jurisdictions wants to have to negotiate with all their neighbors to make service changes to routes that start and end within their own borders.
DC's MetroRail system has a very large share of rides that begin in one jurisdiction and end in another, so it makes a lot of sense for it all to be managed centrally by WMATA. But I suspect there aren't a lot of commuter train rides that begin in Connecticut and end in Suffolk County (or that start in Baltimore and end in Prince William County). Given that, just how would a MetroNorth/LIRR merger help riders?
The main benefit from the proposed merger would be solving issues with Penn Station: you could eliminate some of the separate concourses, easing overcrowding; by through-running trains, you could also increase the number of trains serviced without having to build an expensive new station.
DC's MetroRail system has a very large share of rides that begin in one jurisdiction and end in another, so it makes a lot of sense for it all to be managed centrally by WMATA. But I suspect there aren't a lot of commuter train rides that begin in Connecticut and end in Suffolk County (or that start in Baltimore and end in Prince William County). Given that, just how would a MetroNorth/LIRR merger help riders?