Regarding the problem of huge engines becoming damage sinks, it may be necessary to give diminishing returns on HTK as engines grow larger. Or to give engines a similar stat like what magazines have to boost their HTK.
Actually, although I understand it'd likely be too much of a bother, I'd like the ability to define an 'inner' and an 'outer' armour belt, and define per part type what is inside and what's outside. It'd make all or nothing armour schemes possible, with the bridge, magazines, engines and powerplants inside the inner armour belt, everything else outside the inner armour belt, and maybe thin armour protecting the outside. But then you'd need to figure out how to handle HTK in the outside layer.