Eh, strikecraft really are extremely imbalanced when used en masse. I always like ot have a fleet primarially composed of two heavy carriers and a dozen or so light carriers, with a ratio of 1:3 fighters / bombers.
When playing as Vasari, my bombers can destroy any capital ship in two passes. Nothing short of fifty plus anti-fighter frigates will even stand a chance of stopping this onslaught, and while they're busy tangling with the strikecraft, I'm just chugging out more and more, replicating my carriers, etc. I've taken down whole fleets with this carrier group and lost only a couple transports.
The problem is there just isn't an effective counter to strikecraft. Anti-fighter frigates only destroy one and damage a couple strikecraft when they fly by, and since they have such large, arcing flight paths, it results in low DPS output from the frigates. IE: Bombers fly past a Flak Frigate. Flak shoots at bombers, damages them. Bombers proceed to shoot their target, and fly past. Bombers loop around, shoot target again, and pass target. Bombers fly back in range of anti-strikecraft frigate and get shot again. Not very effective.
Fighters are the same way - they have a low ROF, meaning generally they'll chase a squadron, fire, and then disengage and do one of those annoying, huge loops, and then turn to reengage and have to play catch-up. Finally, every race has at least captial ship with one massive anti-fighter AOE ability. The problem is, obviously, the fighters have to be around the specific capital ship, and you actually need to time it so it hits a large group. Due to the cooldowns and antimatter drain, relying on the capital ship abilities (some of which are less than useful) is impractical.
Frankly I wish we had some Homeworld-style anti-fighter frigates. IE: the Flak Frigate that obliterated bunched groups of fighters, the Drone Frigate that would individually target them...
the only thing that gets annoying is that they break of of your intended destination and pursue a fighter on the other side of the grav-well... that is probably the only reason why flaks are not being used, their damage vs strikecraft is fine as it is, range is short as it should be, autotarget is what messes it up, they'll run out of the battle pursueing a single squad. even though there are 20 bombers right behind him..., and so do all the other flaks...
"wish they'd fix targeting... al ships should target close-by ships first... then when priority target "flak vs strikecraft / LRM vs LF" enters a certain range it'll autotarget, when the unit leaves a certain range (runs or is destroyed), a new target is picked using the same commands as before....."
While I'm not sure that this will be too effective on the issue of flaks, it *IS* something the devs need to look at - I really wish there was something like an 'attack-move' that would attack whatever was closest - when I have a large fleet that is extremely close or even INSIDE an enemy fleet, kill efficiency drops as the entire fleet likes to auto-target the same thing, meaning ships are slowly maneuvering around, slowly spinning in place, capital ships are performing massive loops, all so every ship can shoot the same heavy cruiser. The result is 50,000% overkill, wasting a LOT of time and firepower.