I am going to add Auxiliary Control, Main Engineering, CIC, Primary Flight Operations and Science Department as new modules. Each one makes a different officer available to be recruited to the ship (XO, Chief Engineer, Tactical Officer, Commander Air Group and Science Officer) and will add 1 to the Control Rating of the ship. These requirements add the effect of larger control spaces while maintaining some variety. An officer can be killed if his station is damaged. I may also add 'temporary promotions' if the commander is killed, with the most senior surviving officer taking over as commander until relieved or promoted. The modules will also affect the minimum commander rank for the ship.
I am also going to change how certain bonuses are applied. The commander of a ship will only apply half his bonus for Crew Training, Survey, Fighter Operations, Engineering (new skill) and Tactical (new skill), with the appropriate officer applying his full bonus. The commander of the ship is now a jack-of-all-trades, applying a portion of his bonus while the specialists provide the larger bonuses. Larger ships gain an advantage as they can afford the space to accommodate the specialists, while smaller ships have to make do with the commander handling everything (at half efficiency).
A bonus from the Chief Engineer will only apply if Main Engineering is undamaged. A bonus from the Science Officer will only apply if the Science Department is undamaged. A bonus from the Tactical Officer will only apply if CIC is undamaged. A bonus from the Commander, Air Group will only apply if Primary Flight Operations is undamaged. Bonuses from the commander and XO will only apply if the ship has a control rating greater than zero (they can command the ship from any of the surviving control spaces).
If this works OK, I might add other officers in the future and modify other bonuses in the same way.
I like this solution. I do think, however, that there should be a bit of scaling for the modules.
I don't know how big you plan the modules to be. But I think it would make a lot of sense if the bonuses they grant would also be somewhat dependant on size.
Let us say I make a 300.000 tons battlecruiser. I hardly think that Main Engineering could be a 50 tons module. Because it does not make sense, and also in that case I can just add EVERY module at a minimal cost to large ships, without any effort at all.
In my mind there's 2 possible solutions to this:
1 - The necessary module size is based on ship size, as a percentage. In the above example, you add "Main Engineering blocks" until you've reached, say, 50 tons or 1% of the ship (whichever is bigger). This also result in some more crew (the officer's aides)
2 - You make multiple versions of each module. A "base module" that is small, a "large module" that gives a little bit of bonus, and a "largest module" that give even more bonus. This would encourage to build larger modules on bigger ships. And here too, the largest versions would need some crew, the officer's aides.
Personally, I would prefer solution number 2.
I understand this complicates things a bit, but I think it's necessary to prevent the abuse that would happen if modules had a fixed size. Where every ship above a certain size would have every module at full efficiency, without any kind of tradeoff