New York City has the best public transportation system in the country, but it brings people in and out of Manhattan, which is a limitation for people living in the region and is the main reason for the station being overcrowded within Manhattan.
New Jersey Transit(Orange Line), terminating at Penn Station. Long Island Railroad(Red Line), also terminating at Penn Station. In this context, even Penn Station has the capability to be an efficient through station, it is under-utilized as a terminal for both NJ Tansit and LIRR, which creating inefficiencies.
The call-out is showing MTA, NJ Transit and AMTRAK, three groups are operating the tracks and these tracks are usually competing with each other, which cause delay and cost more in maintenance.
Besides, another layer is 100 year flood zone, although not directly impact the station, showing that Penn Station is under the threat of heavy raining and flash flood issue.