Not sure if this is even possible. I just thought it would make for one heck of a wild ride.
I think I saw somewhere that they were thinking about making, or someone had suggested that they make "Hero" types for GalCiv. Whether that was meant for ships being the "Hero" type or an actual individual is unknown to me.
So here is my Idea....
Say you built a fighting ship and sent it out on patrol. For some unknown reason the captain and crew go rouge and make a preemptive strike on another Civ, causing an international incident and throwing the two governments into bitter war. I guess something like the ambassador getting knocked off, in the galaxy changing events we currently have. Now let us say for an example you are watching over the galaxy, you happen to see one of your own ships speeding away in a direction, you know for a fact, you did not give orders for. Now you must intercept and destroy your own ship.
Also for other reasons you have crews and ships defect to other Civs.
Planets have morale. Maybe we could give morale bonuses and penalties for ship crews, allowing them to fight better or worse during an engagement. How the crew morale would increase could be through victories and or objectives achieved, morale could go down by having other ships lost in battle and just sitting around not doing a damn thing.
Just some crazy ideas. Comments?
P.S. If anyone has thought of these before and posted them, I did not mean to step on any toes.