I find this a typical occurence at legacy stations in large cities. Those stations were not designed to handle the intense volumes of commuters seen at today's rush hours. They were designed to handle something like a 50/50 mix of high density commuters at rush hour and low-density coach and sleeper passengers throughout the day.
You'll find the more modern purpose-designed commuter stations do an incredibly efficient job of funneling commuters off the street and straight to their trains. Specifically, Chicago's LaSalle and Northwestern (Ogilvie) stations. Both were heavily rebuilt in the early 1980's after Amtrak/CNW/RI left and only commuter trains were left. You go in, you go up broad steps or multiple escalators to a broad concourse, and you choose your track. I rarely see people loitering. Most people have monthly passes so only 5-10% of passengers visit the ticket window.
Frankly, stations like NYP and CUS are the worst - not only are they not designed as commuter stations despite their high volume of commuters, they aren't even designed as train stations. They are a commercial/sporting venue with a forgotten trains station underneath, leading to a mish-mash labyrinth of corridors and inefficient waiting rooms. This was done under PRR/PC management when money was tight and passengers didn't matter. It's a reality we're stuck with.
The new Acela: It's not Aveliable.