Obviously a significant increase in fleet supply (options beyond large) would be necessary to balance the higher capitol crews. I like big fleets and my computer handles them pretty much fine. having this done in the staring menu means that mods could be bypassed,which means modders could focus more on other great additions.

I would want ships/structures to break in different parts and crash into the planet when destroyed, instead of just exploding inside the gravity well. After all, the ship/structure IS IN THE GRAVITY WELL so it should be drawn to the planet.

Dynamic experience - Experience gives bonuses based on the enemies faced and the battles outcome. The more a particular capital ship fights say vasari, bonuses are given against that enemy when leveling up. So a shield phase block bonus for example if it has survived many vasari battles or a shield penetration bonus if the ship has won many battles verse the advent.