I have a few ideas as to re-balancing siege and anti-structure frigates...
first, I'd switch their armor type to heavy. Light Frigates are supposed to be their counters, not fighters. Second, give them antimatter pools and abilities that greatly increase their power.
One of the big problems (IIRC) from the early sins siege frigates was that they alternated between being way OP to being fragile useless supply hogs... one person suggested requiring them to take time to start bombing (like, well, actual siege equipment) but this would 1. probably be impractical to implement and 2. remove the possibility of a pop. killing/weak planet bombing raid.
My proposal would be to give them abilities that would greatly increase their power. IIRC there's no ability value to directly alter siege bombing damage- only cooldown- so by, say, doubling damage and cooldown rate (thus keeping same DPS) and then using an over-time ability that consumes AM and halves cooldown you're effectively doubling bombing dps. Other abilities could, for instance, be a channeling AM hog that deals heavy (4X or more the normal damage) DoT bombing but requires a "warm up" and "cool down" (e.g. takes 5 sec. of charging to start, then disables frigate for a few seconds upon ending the ability) which would mimic the "deploy/repack siege gear" thing. Perhaps an ability to double damage/deal extra DoT/pop damage and/or other debuffs but also would decrease shield regen/disable passive regen or something similar (e.g. a Vasari Destructor captain going "channel weapons/shield power to teh lazer of doom!") or perhaps a "double duty" AM heavy ability that "manually fires anti-planet weapons at orbital target, dealing massive damage if it hits" but having say a 50/50 chance of hitting (or something, maybe no penalty if it's just AM expensive), costing heavy AM (limiting other options) and/or disabling the ship/requiring a charge up time.
Essentially such an ability would allow siege frigates to act as makeshift anti-structure frigates, though this would really be an inefficient method, as AM costs (not to mention possible misses/debuffs afterwords) would probably limit to say, 3 or 4 volleys at full AM pool. Just giving them some extra options and mileage.
The same could go for Anti-Structure frigates, e.g. a "channel shields to weapons" or "disable maneuvering engines to stabilize firing arc/targeting" or "deploy secret weapon!" ability, or a "turn torpedoes into makeshift bombs" to add more double-duty versatility.
All of this would, naturally, further increase the Light Frigate's role against these two suckers, as they'd be able to target the AM pool and/or disable abilities (cutting out quite a bit of the extra tactical options) etc.
Also, why not make "copies" of existing strike-craft, making variants for different ship/structures etc. EG a separate fighter type for battleships, carriers etc. These could have different abilities/stats and flavor text/names, e.g. the Antorak Marauder's "[something sinister] Raiders" which would be faster, have greater weapon range and higher raw damage plus perhaps a passive, deal extra damage to structures ability, but have slower turn radius and much looonger build time plus rate of fire, i.e. really good first strike/close to engage and perfect for hit-and-run raids, not so good in prolonged engagements.
A similar fighter type for, say, the Kol, the "Admiral's Guard" or "Kol's Dogs" or just "Interceptors" which would have a passive ability that deals extra damage against SC; they'd have the best raw speed/weapon range/damage of any fighter (possibly firing missiles instead of auto-cannons, should be pretty easy to mod that) but have poor turn speed/rate and the passive ability lowers their evasion (chance to be hit (?) as damage target, remember SC have less than 100% chance to be hit by default, varying by weapon type vs. armor type etc- this can be played with!) so they're devastating at intercepting incoming bombers/fighters in a heavy "first strike" but between poor maneuverability, longer weapon cooldown, and being easier to hit, they'd be at a distinct disadvantage over a protracted dogfight- just like real interceptors vs. fighters. The Sova's SC would be somewhat poorer than others (even TEC's) but be more numerous and build much faster- in essence being the zerg red-shirt human rookies swamping the much more elite but irreplaceable Vasari vets in a painful war of attrition. And of course cruisers could be even cheaper/weaker, so on a one-to-one basis they're outmatched by cap ship fighters; but Hangar defenses/SBs might be cheaper/weaker still, simply having the advantage of expendability/cheapness/numbers/fast build times etc. Or other race or structure specific abilities or trade-offs.
Also, I'm going to try my hand at adding shield meshes to all structures, and also new weapons nodes to cap. ships, to give them anti-fighter turrets. This, too, could add quite a bit of variation- for instance, the Sova's laser defenses would deal anti-light damage, shredding bombers (much more valuable for air superiority and protecting the fleet/itself, then) but sucky damage against ships and structures, so another cap could tear it to pieces relatively easily.
The Battleships would still deal cap. type damage (or composite, perhaps? Not sure how that would compare balance wise) but be relatively weak compared to other cap. weapons in ship-to-ship combat and/or have somewhat lower range plus having poorer accuracy vs. SC etc. So they'd be decent against everything, but not particularly good against anything, though again given the really fast & hard hitting interceptors, all-round toughness and abilities of the battleship it would still be able to hold its own against SC quite admirably, even if it isn't shredding them, just like WWII battleships, which could take insane levels of punishment even from SC and never got sunk while under air escort but would eventually succumb if undefended/unescorted and facing hordes of anti-ship bombers.
