Yeah, the battles between capships are way too short imo. For example, if a BGreen fully hits a Ravana it's down below 50%. Atm in one of the Machina Terra missions I have the problem that the enemy caps die too fast, but if I add an enemy destroyer, the friendly ships die too fast.
In my mod (which uses quite an amount of your ships, Trashman, although with complete different weapons ^^), capital firepower is way smaller and battles last longer. This way the player has a better possibility to react on enemy capitals and his part of gaining victory is much bigger.