so after some inital testing i can't say that carriers are overpowerd against flak frigs.
in some labs tests i have done you need around 2 flaks per carrier to keep the squads down and have enough firepower left over after killing the inital squads, but killing the carriers takes a bit
that is a bit less cash/metal/ore as the carriers cost but far less fleet supply (~50%), if that is balanced is another question.
sure i have lost some flaks to the bombers but less then 10%.
i think it is a problem that the flaks target fighters first but should go after the bombers.
they work best in thight packs and if they are the primary target, so setting them up as a fleet with tight fleet cohesion helps.
that flaks are easily killed by other stuff is another problem, but they are very capable of killing and keeping the squads down and kill the carriers after that.
all tests have been done in a custom map, with spawned ships, so no tech or other ships involved.