I would start all capital ships with 1 weapon unlocked. Research would be required to unlock the 2nd weapon and 3rd weapon if available. Capital weapons would be substantially stronger but would pace with the mid to late game.
I would add additional research to increase the Toughness of capitalships similar to starbase.
I would add a final tier 8 research that would increase the # of targets per bank for Capitalships.
I would add further differentiation in stats between capital ships so they don't all feel the same outside of abilities.