I've been considering something on these lines myself (CIC for Tactical and Auxiliary Control for the XO) but I hadn't thought about Main Engineering or the Science Centre. Good ideas. If these various systems are requirements for the various officers, they would serve to set a minimum rank for the captain of the vessel. I will try to make adding the locations a real decision in terms of costs vs benefit, especially for smaller ships. Main Engineering for example could be 2-3 HS, which would mean the benefits of a Chief Engineer (damage control, potential for instant repair, improvement in maintenance, etc.) would likely be less than an equivalent amount of engineering spaces on smaller vessels.
I will definitely add a check for casualties if the bridge, or any of the other locations, is hit. The idea of an armoured bridge is a good one too. If the location for the individual officers is damaged, any benefits from that officer would no longer apply.
Some random thoughts:
A less "all or nothing" (in terms of benefits) version of this would allow e.g. XO to be assigned if there were a bridge but no aux control, but e.g. with a reduced bonus. So the idea here is that, for a bridge, all officers are in one spot which could be armored more efficiently than individual control stations but knocks out all officer bonuses (and maybe kills/injures them as well) if destroyed vs. having individual stations.
On fighters/FACs: I still like the idea of having a "cockpit". Combined with the above, maybe this means that there are two types of individual stations: reduced and normal size. So for fighters, the command pilot would sit in a reduced size pilot station, while for FAC maybe there would be multiple reduced size individual stations or a reduced-size bridge, while for a DD there might be a full-size bridge and for a BB full-size duty stations.
This also brings up the point that for a fighter, you'd like the command pilot to handle both piloting duties (fighter ops bonus, which applies even to starships?) and command duties (CIC?). Can one officer occupy two stations simultaneously? It almost feels like the ship component here is a duty station that has attributes such as command station (CIC) or plot station (fighter ops which might morph into piloting). Of course this would probably make the assignment AI and micromanagement a lot worse.
Obviously the above is a bit fuzzy in my own head
It feels like bigger ships should require more bridge infrastructure though. So what about a log scale:
<1000 tons: tiny officer stations
<10,000 tons: small officer stations (twice as big?)
<100,000 tons: regular officer stations (another 2x?)
<1,000,000 tons: large officer stations
You could also put a soft cutoff in place for the size restrictions above: one could still use a tiny station on a 1050 ship, it would just have the bonuses reduced by 5%.
John