Please note that this is all we've seen of the game, and it's just an inference of what we are seeing.
I think you're right OP, aesthetically the location seems like a spent opportunity. I'd have liked to see a composite of http://1.bp.blogspot.com/-8J-uc6YF_K0/TZPOgjao90I/AAAAAAAAANc/B4RqDf8fNcU/s1600/2001SpaceOdyssey025.jpg.jpeg, http://imglib.lbl.gov/ImgLib/COLLECTIONS/BERKELEY-LAB/ACCELERATORS/BEVATRON/images/97502207.lowres.jpeg, and http://i282.photobucket.com/albums/kk260/jct5/pict84.jpg. Just tone down the green in the Necron tomb, so it doesn't look like the Emerald Palace, and add more "space-age," white surfaces. The eggheads can still color coordinate the rooms, based on hokey color and emotion science. The ODYSSEUS, CPU room is green, the color of life and sapience. Blue in the labs, to foster a tranquil workforce. Finally, red in the showboat, sales department, where the military brass and DoD can lounge and talk big figures with the sales rep. Their every need is fulfilled by a staff of skilled courtesans.
By layering the facility this way - the deepest layer being the CPU - the facility becomes like a tomb, like an impossible http://en.wikipedia.org/wiki/Qin_Shi_Huang#Mausoleum_of_the_First_emperor. As levels of the Big Empty are unlocked, the old world veneer peels away, and the Courier stands in the presence of an insane AI.