This was one of the really cool things about Empire at War - different characters had bonuses to the entire fleet... like having Grand Moff Tarkin in a fleet gave everyone 10% more fire power or something.
I'd like to see this as you gain levels and actually make the capital ships more like characters... because that's really what a capital ship is - it's one ship that enhances the entire fleet it's a part of, not just one big tank. It would be cool have trees like:
-> Offense
---> Missles (level x)
---> Lasers (level x)
---> Fighters/Bombers
-----> Bays (level x)
-----> Damage modifier (level x)
-> Defense
---> Shield Recharge Rate (level x)
---> Deployable Missile Platforms (level x)
---> (you get the idea...)
-> Fleet Bonuses
---> Damage modifier (level x)
---> Maneuverability (level x)
---> Speed (level x)
---> Range (level x)
Then when you build the initial ship, you'd choose just like you do now - and each one would have different numbers in these given areas... but then from there, when you level a ship up, you can choose where you want to dump your points in. That way you actually customize your capitol ships, so your level 10 carrier may not be anything like someone else's level 10 carrier!
... sort of like how the space stations were in GalCiv II, but mobile

Anyway, just my two cents
/dak