I think an obstacle course for the MTF/ Security guys would be cool. It would be abandoned and you would have to crawl under some stuff, and go through one of those plywood buildings. Also it could have pop up targets that look like 173 or 106 to scare the player, maybe they'd make a loud surprising buzzing noise when you go near it? I suppose you could also do a tear gas room that you'd have run through to get to the end. I figure it could be pretty intense have 173 or 106 chasing you through it, maybe even put 96 in the middle and make him roam around the course.http://youtu.be/_Z84AOHUFC8
The video kinda shows what I mean, make it darker, and less... shooty and I think it'd be pretty darn cool.

Warehouse
Garage with armoured vehicles
A power room (room with something like a hydrodam or nuclear reactor)
Tesla coil room.

A Library.
Ammuniton Depot, they need to put all that ammo somewhere.
Private Quarters.

Autopsy Room [ Used for finding out how an SCP killed a D-Class etc. Could have a Corpse or two. Perhaps even Body Bags. ]

Medical Bay [ Random chance of finding Medi-Kits and Eye Drops. ]

Vehicle Bay [ Helicopters, Cars, Other Transportation Methods. All Locked Down. ]

Sewers and Plumbing System [ Surely they must need this? Could be abandoned ones too with a risk of 106 spawning. ]

Security Terminals [ Used for Clearance to another part of the Facility. Could be secured by Cameras or Trip Lasers, Resulting in the Player having to try to disable it or sneak around to avoid risk of being killed. ]

Stairwells [ Lead to another " Floor " similar to the Elevators. Adds realism. ]

Rooftops [ Adds realism. Could have Doors leading to another part of the Facility. Fall off would mean death. A Helicopter could patrol above. ]

Data Storage [ Several Computers, Terminals and other types of Storage for Data. Most would be off but some could be on and provide interesting details about the Foundation and SCPs. ]

D-Class Corridor [ Locked Doors for D-Class Cells. Adds realism. ]

Broken Corridor [ Possibly destroyed by 682 rampaging through or by another SCP. Could have holes in the ground that the Player must side step to avoid falling down. Falling down could either mean death or to a lower floor while sustaining injury. ]

Broken Corridor B [ Several broken pipes or wires, Giving off extremely Hot Steam or Electricity Sparks respectively. Might require trying to disable the obstacles through a Valve or Switchbox. Crouching under neath Steam may be a possibility. ]

Abandoned Garage [ A simple, dark Garage. Doors leading outside are locked tight. A chance for 106 to spawn If the Player lingers for too long. ]

Air Ducts [ Could provide a means of getting around the Facility, Though limited to crouching. 173 could appear in Larger Air Ducts where Player can walk. Rats and Flies could appear for ambience and realism. ]

Cafeteria [ Tables, Chairs, Benches, Foodstalls etc. Very little Food could be eaten when Injured similar to Medi-Kits but work over time. Would probably be scraps or small food. Not exactly Cakes and Pizza. ]

Entrance Hall / Atrium [ A Large Hall similar to Gate A. Has a Big Skylight across the Ceiling and Stairs leading downwards to a Lower Section. To the Right and Left are Doors leading to other parts of the Facility. ]