Joshua, another good thing captured fighters/captured capships are good for is surprise attacks against opposing forces - the opposing forces don't suspect one of their own will attack them so they don't fire on them. You can take a captured capship/fighter and move it right next to an opposing unit and then open fire. Another thing to do is to move the captured fighters captured capships in front of Confed fighters & Confed ships to make it look like they're being chased. Then when Kilrathi reinforcements come to help out to attack the pursuing Confed units, ambush the Kilrathi units with the captured units. Also, the more units you capture, the more the Kilrathi (or whoever is opposing you) has to keep track of. This can confuse them more. What I'd like to do is when the shields on a Kilrathi capship are down is to use a paintgun to spray paint over the hull some grafitti like "Kilrathi are stupid" just to tick off Kilrathi. I think that would be a new addition to Wing Commander -- the paint gun -- that could be used to anger Kilrathi to divert them away from objects the player has to save like transports, starbases, capships, Confed fighters, etc. The paintgun could also be used to blind the pilot by painting over its canopy. What's nifty about the paintgun is that the paint to weight ratio is very high -- you could spray lots and lots of paint before you'd run out. Most likely, the Kilrathi would fly back to its capship after it gets blinded to have tech people scrub the paint off. That would take much time because paint is hard to scrub off, scraping it off would scratch the windshield of the canopy so it would have to be scrubbed off. This could be interesting -- just knock down the nose shields on a fighter, hit the nose with some paint to blind the Kilrathi pilot, Kilrathi pilot then uses computer to plot a course back to his capship and you can follow the fighter to find the capship to destroy it or capture it (your choice).
Also, since capturing a ship takes more courage and more skill than simply destroying it, there could be medals given out to player characters who capture capships & fighters -- they would be worth more than the ones for destroying fighters. That's what I liked about WC1 was being given medals.