Hey there
I wonder of whatabouts of this idea. Is it still alive ?
I always wanted to make something like this and I have many combat systems in my notebook that came to my mind at that time. But I would prefer turn based system, somehow. I have some ideas in my mind. It would have simple interface, however many possible choices of crew skills, maneuvers and options. Crew would get new abilities with experience (and game could be very character oriented), for example:
if enginer can learn to perform, lets say, a Energy Discharge, then he can tranfer energy from guns to shield at any moment (this would work like interrupt in card games, so to every your action there could be reaction and vice versa) and in emergency save ship from some big damage that could occur.
These abilities (crew, commander-you, and ship has) would have cooldown and after performing there will be time in turns to make them available again (different for different abilities, some fast, some once per combat, etc), and they could have cost in energy or other things to perform (so maybe you would have to have some usable up equipment to perform them). So it would be very tactical in deciding what to use if you are not sure of skill (and abilities) of enemy crew, if they have some ship modifications (that allow performing this or that action) or what to hold in reserve, or simply how much energy spent on certain abilities. Many kinds of equipmemnt could also allow special actions, like scanners to see what systems enemy ship has (what abilities, counter abilities can use against you etc), and all sorts of common stuff like ecm, jamming etc.
But the main thing would be what special abilties (with cooldown) different types of ships, crew and characters can perform. For example:
high level gunner could learn skill named, mmm, Deadly Aim (or whatever, heh..) that gives 75% chance for critical hit on enemy ship once per battle (or say, every 10 turns). Unfortunately, this could be countered by enemys ship special ability of Enhanced Armor which can make any crit hit a normal one. But luckily, you disabled possibility for special action on enemy ship with your Ion Gun shot... etc.
Add to this energy maintaining and allocation, and standard stats like weapons damage, shields, hull ond other. To simplify play you could in your turn mark to what counter abilities you give energy (so they could be automaticaly used in enemys turn) or what ability your crew prepare (which means that character can't do anything else this turn). So, in your turn you would just make few clicks..and thats all. Simple. And lots of tactics.
I don't know if you still want to that however