Rid the ship of the elevator, replace it with stairs.
Private living quarters only for the Captain, First Officer and Chief Engineer. Junior officers should at least double up and most of the crew be in bunk rooms.
Put a big thick armored door that swings closed in front of the regular inner doors to the air locks. Something with a manual latch, it's way to easy to board that ship simply by docking with it.
I'd make the majority of the corridors narrower.