I think an issue with cap ships is the triple growth curves they have on levelling up. Cap ships, when they level up gain:
- Extra shields and hull. Basic health.
- Extra max mitigation and armor points. Two health multipliers.
- Extra shields, health, armor, and maybe mitigation through research. Multipliers on top.
- Extra base weapon damage. Basic DPS.
- Extra weapon fire rate. More DPS Multipliers.
- Increased weapon damage from research. DPS multipliers.
- More powerful and effiicient abilities.
- More antimatter and quicker antimatter recharge.
- More AM storage and recharge through research, to grant even more excellent abilities.
What you get is a unit that is rather unremarkable at level one, which advances to absolutely awesome at max level. The research bonuses tend to balance out across the board, although Advent's mitigation boost is awesome for their cap ships.
So yeah, capital ships seem to suck at the low levels, and they really do. They are equally bad if you build them just to add to an endgame fleet. But that's because capital ships are a long term investment. You can't expect to fill your fleet with level 1-4 cap ships, then expect the caps to excel. It'll never happen.