...the crew member rooms for "R. Hunter" and "M. Kusanagi"?

I chuckled when I saw that. There's also one for who I believe is the girl commander from Martian Successor Nadesico.

Very cute little references.

I'm happy to say, it's one of the first things I noticed about this game years ago, and it pleased me to no end.

Yea. I recognized a couple more too. "N. Izumi" and "A. Shinohara" are Noa Izumi and Asuma Shinohara from Patlabor. There is one more door there though, and I have no clue who that one is supposed to be.

Speaking of M. Kusanagi, I saw that one of the companies in first city is called "Batou"

Another one i spotted was in the game manual. One of the founding companies of the UCA is Armacham, which some will remember is the name of the company you investigate in FEAR. I guess they liked the name and used it again in fear :P

Yup. I also noticed I. Dyson. Its Isamu Dyson From Macross Plus ;)

https://www.youtube.com/watch?v=xmX08CsXqws