I know bunkers can be very samey but I guess military complexes are built to a purpose and not to look glam.
Few ideas that may be of interest…
Flooded areas that can negate any kind of noise reduction bonus
The one place I was impressed with was the Hellmouth, the big bunker/garage thing … so how about a coastal military complex with a sub dock or the like … maybe allowing boats to row between islands.
Maybe a “run the gauntlet” mission that you infiltrate a production lab where you have to blow it up or the like collect bits maybe even re-program a tick or a runner to become a “pet”, or maybe you get to see parts being made for a future add in robot or the like.
How about a super massive bunker with a transport facility (Maybe opening out to missile sylos), you could find either hand carts or maybe jury rig some small electrical buggies to transport you from one “station” to the next, this then could allow the game to have abandoned rail yards above ground like you get to see in S.T.A.L.K.E.R
Some nicely epic underground complexes and rooms not just corridor, corridor, corridor rince and repeat