First of all I understand this 'idea' would require a major rework for a somewhat minor change, so naturally it wouldn't a priority, but this idea i had when I used to play original X-Com and still remains a valid idea in this. plenty of times i had to build rooms next to say hangers, but really wish they wasn't acess to those rooms from the hangers
Customised Room Access Tunnels:
Instead of automatically have a tunnel to access every room next to a facility, set it up so each room has only between 1-4 access tunnels customisable by the player, this would mean you can have room that are next to each other, but with no access tunnel, meaning you and the aliens would have to go the long way around to get to the room.
In terms of base function it would have no effect, but in term of base defence it would allow a much more tactical design of clear entry point, clear choke point and ambush points, even in a base that is compleately full