When someone does bomber spam, you really cant counter fast enough with flak unless you have 100+ flak.

I counter mass bombers with 20% fighters, 30% flak, and the rest LF.

Its better to kill the carriers then try to stop the bombers.

Jep, the carriers need to go fast. Focusfire on them, use abilites, crunch them together. Once they are gone the bombers are just free XP to be harvested.

Can't wait till vasari are playable, I miss them phasic traps. They made this so much easier.

Yes I agree with that. But it doesn't mean flaks can not punish the bombers more or less, instead being screwed by them.

And I also found that, if rushing with Halcyon, it is possible to use 4 bomber squadrons, flaks just can be ignored totally.

What I suggest, is actually to add a mid game HP/damage buff tech to some early ships - flaks, LFs, or even scouts. That will be more flexible to adjust the balance, since the situation in early game is quite different from the mid / late game, since the early ships will then facing different and more diversified enemies.

That's also what I mean. The HP/damage upgrade should be a "fine" adjustment, the only reason is enhance the necessity of early units a little.

The problem is quantity. In a game such like WarCraft 3 it is much easier to resolve the problem, and even in StarCraft it is still OK. But in Sins, in such a relatively larger scale of battle, it will be either overpowered in swarm or in single.

And it is also similar in the reality, just to remind the history of WWII.

To solve such a problem, I think the solutions may include:

- all units require supplies to operation. And the resupply capacity of any single planet is limited. (But such design will of course ruins any RTS games. It is only appropriate for turn based SLG.)

- decrease the defense of units if they are massed in swarm, and decrease the dodge: due to the limit of on-field C4IS ability, and it is difficult to cooperate so many units in the battlefield. (This will still greatly change the mechanics. And it is also redundant considering the existing mitigation system.)

- if only concerns the bomber problems, introduce a third strikecraft "interceptor", with low maneuvability (low dodge rate and low turn rate), high linear accelerate rate, longer shoot range than bombers, and has extra damage to the bombers. (But it is really a disaster to balance even more unit types.)

- set the fighters and flaks as using different weapons: to ship, no change; to SCs only, use explosive salvos. (The "first-kicking-everyone's-ass-to-hell-attack-wave" problem is still there.)

- decrease the supply limit directly. (Ohhhhhhhh nooooooooooooo! I swear I will immediately create my own mod if they really do this!)

So currently I have no idea about the problem.

I think there should be tech that restores 3/4 of the flaks original stat, but needs a couple cruiser prerequisites and costs the same as the kodiak cruiser tech, would mean they still have a place but that you cant get them to a spamming stage before you can spend your resources on a much better fleet combination. 

Also I have never had problems vs mass bombers, in my fleets I always start with a carrier at the beginning of the game and its always my flagship, and in a fleet build of mine I always have 2-3 support carriers with 2 squadrons of fighters each, that combined with some logistical ships and bombers don't seem to actually do any damage, even with a horde of them hitting my fleet. 

Well, to present a hard counter in science fiction to the Battlestar Galactica example I reference the Bolo series, in which light attack craft do not stand a chance against relavistic speed Hellbore fire. The armor, shielding, and resiliency of a heavy planetary siege unit clearly outweighs the mobility advantage offered by a lighter, more nimble air/space vehicle, as does power generation and tracking abilities. You can see many battles where careful application of firepower, positioning, and ability to soak up damage  overcomes more numerous, lighter armed foes. They are simply not able to match an attrition rate that outweighed the cost of a fewer heavy units with multiple lines of defense. The best winning tactic was the Melconians planetary razing strategy (yes, yes, I suppose the carrier analogy still works if we conceptualize planets as carriers and everything they produce as strikecraft - clearly destroying the planet means all it produced will be cut off from support) but even they did not clearly win against Bolos and the Concordiat. I know that some might say the Bolo series is merely a God mod for tanks, but I think it serves as an excellent example of what to use for balancing a game.