If you don't have Carriers you should still be able to beat them with Flaks. Right now, it seems carriers are somewhat of a prerequisite- I'd like not to make them if I don't want to.
Why? Fighters killing bombers has been the way of war since their inception. Anti-air ground sites are the last line of defense, used because your actual defense failed. When bombers are already on your territory, it's too late. They're dealing damage. You're matching a ground site designed to kill airplanes against an airplane designed to kill ground sites. It's an even match depending on technology.
It's entirely sensible that flak frigates would only be relatively equal against bombers, it's the expected result. You're pitting strike craft design to kill frigates against frigates designed to kill strike craft. As they are equivalently priced for a numerical advantage in the much maligned Vasari v Advent matchup, I fail to see why even numbers leading to the loss of the defense frigates should be anything but expected. To be otherwise makes strike craft useless.
1. Gamplay > History- Although, your example isn't really accurate. A) Flaks aren't ground units. 
Naval AA vessels significantly outrange aircraft. C) The described purpose of a Flak is to "Protect the fleet" NOT "protect bombers."
2. While your logic is sensible-
Flak = Frigate
Bomber = Strikesquad
Bomber > Frigate
Flak > Strikesquad
Then,
Bomber ~= Flak
It's narrowminded. The bomber has more utility, thus it's value is greater. You can counter flak with Bombers if you just muscle them down because they 'break even', as a result- Bombers are much better than flaks.
Bomber ~= Flak
Bomber > Frigate!Flak
Frigate!Flak > Flak
Bomber > Frigate
Bomber > Flak
So... the only practical counter for Bombers are Fighters, and fighters don't really beat anything else, sure- that almost makes sense... but wait... It's wrong to think of Bombers as a unit in and of themselves; they're just a part of the Carrier. So when we say fighters are the only real counter to bombers, what we're really saying is that carriers are the only counter to carriers.
Fighter > Bomber
Carrier.fighter > Carrier.bomber
Carrier > Carrier
So, lets take all of my p, q expressions up till now and make one point that's rather self-evident.
Carrier.bomber > Frigate
Carrier.fighter > Carrier.bomber
Carrier ~= Carrier
Carrier > Frigate
Logically, it's STUPID if Flaks don't beat Bombers, otherwise Carriers are the only unit worth making. Are all of these expressions true in terms of the game? Gee, I have no clue (testing the counter system in this game is troublesome with so many variables to consider- Armor, Hull regen, Shield regen, shield Mitigation, etc- another thing that makes playing this game confusing for multiplayer)- but If Flaks are breaking even with Bombers, then that makes Carriers the only unit worth making- and that makes for a poor game.
