Mr. Lensovet, Take any transportation facility and put double the number of trains and passengers it was designed to handle and you have Penn as it exists today. Add MSG (entertainment venue, not food seasoning) and the Ponn Plaza office buildings, and you've just added more fuel to the fire.
Remember, only PRR intercity operated in there when it opened, having changed their steam engines for third rail electrics (DD-1's) at Manhattan Transfer (today, an NJT maintenance facility).
LIRR? get into Suffolk County and you were talking farmland.
Finally, anyone who thinks "the place is a dump" today, should have seen the LIRR side circa, say, the 40's and even 50's (I did). The LIRR side had all the aesthetics of an NYCTA subway station.