I think there are three reasonable options:
1} Rebalance them as normal-cap ships (the easy way out).
2} Buff their damage so initial cap-dps is higher than a non-swarmer cap.
3} Rebalance them with absolutely huge caps (3 to 5 times their current size) to take advantage of overkill.
Agreed. 2 is the option i find the best.
Thus, I would go for option 2.
Unfortunately, option 2 is already implemented.
The swarmers have 10-80% more Cap DPS than Fighters, and many of them have special abilities as well. Cloaking, FF Immunity, etc.
I suppose you could ask for 100% DPS above fighters level damage, or maybe 10x multipliers?
That's about what it'd take to make Swarmers have enough advantages to overcome the disadvantages.
Swarmers are, for example, about the only place that Armor matters.
Laser Gatlings have good DPS for a swarmer, 600/sec. A Fighter I is 1020/sec. The Gatling is 60% of the Fighter's DPS, and has almost 3x the cap.
Yet it takes 1301 Gatlings to kill a Fortress I, while only taking 415 Fighters. That's because the swarmers all fire lots of weak shots, so Armor can actually matter.
Swarmers suffer worse DPS deterioration than lower cap ship types.
As mentioned, Swarmers cause the game engine to cry in pain when you've unlocked Mk I - Mk IV of one or two types of swarmer.
If you made Swarmers a high-alpha unit (10,000 damage, 15 sec reload) they might be more useful... but I dunno about that.