Maybe add a bit more customization for the ship itself? Like give it guns for it to have on it's own, maybe allow a custom flag-ship(only one custom ship allowed plus one custom fighter unit) and a more in-depth fighting system such as a large play-field and objectives such as neutralizing enemy bases and ships as well.
Would make the game extremely addicting especially if given an online-competitive element to it as well.
Custom ships, custom stats, custom guns, shields etc. just limited to how much can be customized. But no limit to the strength and abilities you can make custom ships even being able to constantly go back to them and make them better, stronger, even giving skill trees for the commander themselves as they level up to unlock passive abilities, active abilities, even passive upgrades as well to all units would be nice too.