Just some ideas I've had floating around on how to balance the AI and make it not so omnipotent. These can be taken as one big change or picking and choosing ideas that seem good. Let me know if they're terrible.
AI can no longer track people with cameras. Having to manually locate people makes it significantly less omnipotent. Possibly also take away the free moving camera in favor of only being able to jump to different security cameras (last part would need to be tested. Might be overly tedious for the player.)
AI now has two "modes". Camera mode and hologram mode.
Camera mode allows it to use the cameras as it normally would, but it cannot physically interact with the station (cannot bolt doors and cannot access machinery)
Hologram mode allows it to physically bolt doors of the room the holopad is in and allows it to access machinery in that room.
Holopads can be destroyed by crew members, making it so the AI cannot physically interact with the room until it's fixed
I have a final idea but I'm not sure where it would fit in:
Maybe through tampering with cameras, maybe through some kind of privacy button in certain rooms, but making it so all the people in that room appear as the grey blur silhouette that drones see