Not sure if this has come up or not, but it's a thought that I had while playing last night. I love the fact that the cap ships gain experience and unlock new abilities. It's a great idea that a ship and crew that have been to hell and back become pretty bad-ass. However, what I thought about was all the other ships.
I had a fleet that included as few frigates and cruisers that lasted through most of the game, undefeated. It would be great if they could get some sort of "veteran" status. No need for unlocked special abilities or anything, but simply some sort of combat modifier to signify the fact that they've fought a bunch of battles. (After all, even in space, experienced naval crews aren't restricted to cap-ships.)
(I'd also love the ability to pick my own name for cap ships.)