Well, if you've already got the systems in place, shouldn't be too hard too add a few extra types of stuff to it. The crew AI in reacting to them would be the hard part. And enemy AI.
Which leads us to grenades, or more specifically, gas grenades. Toss one in to a room, wait for the enemy to come running out, straight into your pre-planned ambush.
Grenades were a bit weird in Xcom, either being uber powerful or mostly useless, depending on the terrain. But in the always enclosed environment of ships, they might work great. You mostly wouldn't want to use really heavy explosives (in case you all suddenly ended up outside the ship through the hole you made in it), but smoke/poison/acid mist would dovetail in nicely with the gas and door containment system mentioned. More-or-less a "bring your own little portable gas trap", rather than a kaboom.
Sort of like those opening scenes of Starwars, where they smoke the corridor and Darth Vader comes storming in, and the Rebels just pretty much decide that they're screwed. Sure, Darth had a part to play in this, but Rebels with smoke-induced Stormtrooper aim would have surrendered to an etiquette droid at that point. Might make for some interesting strategies and crew make-up decisions, offensively or defensively. As well as making things like going directly for control rooms and air management rooms just as vital as hitting the weapons or shields in some scenarios. On attack or defense.
But it'd be a bugger to program the enemy AI to take advantage of it, rather than just have them break those control rooms entirely. Running away from contamination is easy, but having the AI proactively open a door, chuck in a grenade, and then seal the room (with you in it) is hard. Maybe just rely on it being an immergent scenario, where the player's reactions make the AI seem way smarter than it is. So they probably will gas themselves sometimes, which is silly, but hilarious.
Is there going to be a hacker/engineer style class or set of items?