Would be nice if dev did it, but I know realistically, its a slim chance. As a mod, I guess limits can be put on either hull size or weapons or both. Don't want to limit colony ships or non-combat ships though.
Maybe have it where every colony automatically produce a specific resource that can be used to build 1 capital ship. So bigger empires have more capital ships, but the cost of building that capital ships would be very high and would lower morale during the time it is being built. If at any time the colony is lost, the cost of maintaining the Captital ship would be tremendous and would penalize empire moral and money. The mechanic for this could be that once a colony is settled, it produces 1 resource that is needed to build that capital ship. That resource also produces morale. When the capital ship is built, the capital ship would cost the same amount of morale the resource is producing, thus balancing out. So when a colony is lost, moral takes a dip and maintaining the capital ship would cost the faction.
The faction that takes the colony would now benefit from the resource to build a capital ship and the same method applies.
Also, capital ships should be powerful and not just an oversize version of the medium hull. Capital ships should also produce bonuses to planets and ships they share a sector with.
Well, that's my idea for a mod for it.