Everyone in NYC hates it and we are currently building an extension at the old post office, as it is not fit for usage anymore.
The old one (the one that got demolished in the 60s) was miles ahead in both space and aesthetics. Also, almost nobody hates the Grand Central Station, even though it gets overran with tourists as it is a beautiful peace of work.
1. Amtrak insists on trying to do an airplane-like boarding situation for trains, rather than the traditional practice of telling people what track their train will be on several minutes in advance and letting them wait on the platform. This means you have boarding lines and expectant crowds in places that aren't designed to handle that kind of capacity.
2. Each of the services that call at Penn Station has its own segregated platforms, mezzanine, and ticketing areas, and the connectivity between these is poor and confusing. Although, this is probably driven in large part by...
3. Madison Square Garden was built on top of Penn Station, and a substantial portion of the above-ground infrastructure is dedicated to supporting that tenant rather than the transportation infrastructure.
Penn Station used to have a more normal major-station layout when it was still part of the Pennsylvania Railroad, but that was ruined by the building of Madison Square Garden on top of it.
Penn Station's major issue was that when it was designed and built, intercity traffic was a big deal and commuter traffic was not, and it was designed accordingly. Today the central platforms Amtrak uses are massively oversized and the commuter-rail only platforms to the side take 3-5 full minutes to clear a train.
For example, Strong Towns [1] seems to champion the whole "the suburbs are unsustainable" perspective, but never the "public works projects in HCOL metros are too expensive for the resulting density" thesis. Market forces will likely work it out in this case though (people leaving HCOL locations for lower density locations where per dollar quality of life is higher, with major cities having to do more with less, or do less with less [tax revenue] [2]).
[1] https://www.strongtowns.org/the-growth-ponzi-scheme
[2] https://www.nytimes.com/2020/08/27/nyregion/mta-virus-budget...