Small interior
What about an 1x1 energy generator (perhaps producing 4/2 energy), an 1x1 energy storage (holding 4 energy), a 1x2 cockpit (same as command centre), a 1x1 shieldgenerator (full radius of six square in diameter but not that strong) and an 1x1 airlock.
With these items it might be possible to construct several smaller fighters (4 crewmen > pilot, two weapons, one energy carrier) which might be entered via a shuttlebay on board.
Loss of crew
I've seen that crew outside the ship is not dying. Instead they use the next normal door to re-enter the ship. That's not that good.
Tankdoors/Firedoors
If a section is destroyed normally oxygen would flow out the ship through the normal doors. It might be a nice tweak to "seal" doors by clicking on them. There might be an additional firedoor closing by clicking on a normal door. This door might prevent oxygen from flowing out the ship and blocking the spread of fire.
Additionally crew might not use this door until the player opens the firedoor manually.
Forcefields
Alternatively to firedoors there might be forcefields. They do the same as firedoors (see above) but need energy. They can be activated in every at least 2x1 corridor if there is no normal door. Activation by player click on that section.
