I have a few ideas, add a "activeness" to areas around the map which goes up sometimes caused by either leaving the area or an event and can be reduced by clearing out the monsters that spawn or through a side quest close a vent or destroy spore pods.
Maybe a distraction and stealth mechanic where enemy's chase you to the place they saw you then head in that direction if they cant see you and have ways to lure enemy's away or even distract large enemy's with other female crew trapped on the ship.
also maybe a shop where you buy ammo and stuff but get money through saving girls through out the ship and getting them to safe spots, maybe you could even hire girls to help "fight" or help to interactions that might require two people, maybe have it so you need to give the girls their own ammo to fight with or they can just act as a distraction and if they get too contaminated they become an enemy; if they run out of health then you have to carry them making it hard to defend yourself but they could be left on the floor as a distraction if they aren't fully contaminated but the enemy's to prioritize the player if the NPC is down