I like it.
A couple of module ideas based around controlling heat:
Dedicated Heat Sink modules that need to be placed on the outside of a ship. If they become damaged or destroyed in battle ship components may have to shut down to avoid heat overload, or you could overload them and they start taking heat damage.
Every crew member could add a small amount to the heat output. Which wouldn't matter much in small ships, but with a crew of hundreds, hundreds you'd have to take it seriously.
Heat Packet Gun (Magnetically Insulated Plasma Gun, MIP gun). More expensive than standard heatsinks (which are cheap and have decent armour because they're basically metal radiators), the MIP Gun channels heat energy into an insulated high energy absorption packet and then expels it. The process is expensive and also requires a lot of energy to sustain, which also creates a lot of heat too, so overall it's pretty inefficient. But, it is armoured than heat sinks and able to absorb a lot more energy too. (so you need less of them for the same effect).
The other bonus of the Heat Packet Gun is that it periodically fires a slow moving but highly volatile blob of plasma, which can melt anything it comes into contact with (high damage small explosive radius, low penetration, high chance of starting fires).
Alternatively, plasma from the MIP gun can be stored (like ammo), and use in dedicated weapons systems that can fire the plasma balls faster, more accurately and for longer distances, even be adding some guidance to plasma shots through manipulation of the magnetic packets too (Guided or faster firing plasma would have less damage per hit, as some of the reactive matter is used to give it extra speed).
Finally, storing plasma as ammunition is a dodgy procedure, not only does it explode like other types of ammunition, but it also requires a constant feed of energy to keep the magnetic containers stable. Going for too long with an energy input degrades the magnetic shells, meaning they could spontaneously explode. Also carrying them for too long, between storage and guns, or MIP and Storage, could cause them to explode in transit. And wearing a pair of oven mitts is not going to protect the crew who's holding it at the time.
(For when crew happiness is added, carrying Plasma ammunition has a highly negative effect on morale for whoever is carrying it. Also standing anywhere near plasma ammunition has a negative effect on all crew morale).
