You said it, Vaihlor!
Gods, I love FS2!
I mentioned this in the carrier thread, but I also believe ALL cap ships should have basic flak guns... Historically, all heavy ships had them, and in sci-fi all heavy ships seem to have at least basic automated flak or anti-strike weapons even going back to the original Battlestar Galactica series and Star Wars.
How about a more specific special ability for FLak Frigs...? Something along the lines of "Guard" where you can select a specific ship for the frig to guard and not leave a defined "command radius" of that ship to protect it from incoming strike craft? That would stop them from chasing down carriers and LF's, too. Flak, also, I think should do more damage to bombers than fighters, as fighters are nominally considered far more maneuverable and aren't required to (logically speaking) maintain a heading to ready a launch of bombs. perhaps up bomber damage a bit and require them to positively track their target with a fixed heading for a certain amount of time for targeting purposes and if they fail to hold the track, lose a percentage chance to hit.
Make fighters travel faster and do lighter damage, making them more positively a bomber and fighter hunter...?
Change the cost for fighters and bombers from anti-matter to actual credit, metal, and crystal costs. Minimal, sure, but it would mean something especially in early game rushes when your resources are stretched thin.
Many fleet engagements are usually made or broken by fighter and bomber success/failure. This should hold true with SoaSE, in my opinion. Historically, carriers were the core of the fleet, not battleships as some assume. 1-2 bombers, in the real world, could take out a battleship, or even another carrier, if it could get through with its dropped torpedoes and bombs.
While I'm not advocating making the game "like the real world" in this regard, I
am advocating that strike craft and their nemeses take on more than just a cursory role, unlike the past. I'm sure a balance of some sort can be reached. The only question is where will Ironclad and Stardock find that balance.