Pump room
There could be a burst pipe spraying scalding water blocking passage and turning the water off here could get you through, or if SCP-457 is ever implemented, you could turn the sprinklers on to stop him.

Generator room
To make gate A less easy to get to, maybe you could have to restore power to the elevator by finding the generator room and switching the power on.

Ventilation shaft
You could enter an open air vent and crawl through some shafts to reach another part of the tunnels, but 173 would chase you throughout them (isn't it said he travels through air vents?)

Boiler room
A room full of equipment, water tanks and other stuff that runs the facility, maybe when you enter, 106 or some other SCP would start chasing you and you would have to navigate pipes and platforms to escape.

Elevator shaft
A room that when openned, an elevator will crash down revealing a dead scientist/guard/MTF, if you walk into the elevator before it crashes, you get killed.

Storage room
A large maze like room where the site stores supplies and provisions, like the entrance zone server rooms SCP-173 would spawn here and chase the player, who would have to carefully navigate through it while keeping sight of 173, could have 2 level segments, suggested by Akatos.

096 server room
Suggested by Omniary

Electric center
Suggested by Omniary

Tesla gates
Suggested by Omniary

SCP-229: Wire weed: Would infest a generator room and would kill the player if they touch it, you would have to navigate through by crouching and walking around the wires, you would have to activate the generator to restore power to a door or machine.

This would work with gogerts trolley idea, the generator could restore power to it and provide a shortcut.

SCP-457: The burning man: Could be the SCP that chases you through the boiler room, if you lure it under a leaking pipe it would shrink, if it catches the player it would burn them, if it burns you too long it would set you on fire, suggested by Omniary in another topic here: http://scpcbgame.com/forum/viewtopic.php?f=5&t=3510

SCP-569: Heads: Would float aimlessly in a hall, if the player bumps into them, runs, or causes a loud noise (Radio or ringing SCP-513) they would spray the player down and kill them, crouch walking will not set them off.

SCP-625: Anklebiters: Would attempt to injure the player and cause them too bleed, would only spawn in certain rooms, they're hard to hear and would cause damage without notice, wearing a hazmat suit helps protect you from damage, due to possibly being too overpowered, they could only spawn in a single room and there would be some kind of warning to alert the player to there presence.

SCP-534: Misplaced blood
In a scripted room with pipes, the vents would start releasing SCP-534 into the room, and you would need the hazmat sut to progress or run through before the cells effect you.

SCP-534-1 would injure you if yu remain exposed too long, by damaging body parts.

SCP-534-2 would do the same but would cause bleeding, and eventually death if exposed for too long

SCP-534-3 would slow you down and kill you if inhaled for too long

You could stop this by recontaining SCP-534 in it's containment chamber.

It would be interesting if you could also find SCP-008 victims roaming around here as well.

-Pipes would burst, tiles would fall and smash in a few hallways,

-Some survivors could be attacked by 008 victims in front of the player.