I never gave a crap about any of my ship's captains. Execute popped up...Dead! Never knew their name anyway. Old whats his face just got shot. Oh well! Next. Maybe that's the point of it, but I think it would be interesting to the campaign, if it were the Captains that gain levels instead of the ship.
Spire needed to gain levels before he could add ships to his fleet. Other Captains should need to gain levels before they can add extras to their ship. Has a certain amount of continuity to it.
You would think twice before
Executing that level 10 Admiral! If ever!
I guess the ships are suppose to be the characters. Just saying, when I played the XCOM games, I would rename the squad members to have the names of my family. I really cared about those characters. Such a small thing added weight to my decisions.