This is mostly from multiplayer point of view but mp also speaks volumes about cap balance. Caps get very little use beyond the first one you get for free. Partly because a lvl 1 cap just isn't cost effective compared to frigates or cruisers but also because multiple caps nerf eachother by sharing XP. Generally it's better to have one lvl 6 cap + more fleet than 2 lvl 3 caps.
It would be a level 6 vs 2 level 4 caps owing to how levels work. Two capital ships have a vast advantage in flexibility and antimatter pool. For example player 2 could tailor ship 1 to countering capitals (antimatter drains and status effects) and ship 2 to countering fleets (area damage).
In any case there's no way for a single capital ship to be present at every battle. You should be able to gain more XP overall by having more capital ship. Pirate raids are a case in point.
Also...never heard of the Sova rush? Homeworld embargo for victory! Nothing else in the game will cut your enemies total income in half so easily. And you get the credits to boot.
Advent capital carrier starts with 2 squadrons while a Drone Host has 3. Shouldn't the capital carrier have more.
They'd have to remove firepower from the Halcyon or increase its cost.