I agree that upping flak frigates is the path to take. Carriers may be overpowered, but they're a really cool unit that works very differently from the rest of the unit types. They're good, yes, but don't forget that they're expensive and take a lot of fleet supply. The real problem is that there's no really good counter to carriers except other carriers. Currently, flaks are decent at clearing fighters, but they still don't work very well against bombers. This means that if you want to protect your fleet against a mixed strikecraft fleet, you have to invest in fighters. It's not healthy for a unit's only counter to be more of itself, obviously, and the natural counter to strikecraft are flak frigates.
Of course, flak frigates have a few built-in tactical disadvantages against carriers. For one thing, flak frigates are much slower than the fighters they counter, which gives the carrier owner the ability to choose how, when, and where flak/fighter encounters will take place. Flak frigates also can't really destroy carriers -- only the strikecraft they produce. Think about how this is different from a typical counter, such as LRMs to counter light frigates. Most counters actually eliminate the ships they counter, but flaks leave carriers unhurt and able to retreat to fight another day. Moreover, wheras most unit counters CAN be deployed even when there aren't units to counter, even if they're not optimal, flak frigates are really pretty useless except as carrier stoppers.
I repeat, the answer to this problem is to make flak frigates VERY EFFECTIVE. Flak frigates are useless against anything but carriers, they have built-in disadvantages against carriers, and they can't deal effectively with bombers. The solution is to make flak frigates strong enough that they can TOTALLY SHUT DOWN a carrier fleet of equal or even greater size. That way, carriers can still be strong, cool units, but won't dominate as long as the other player invests fleet supply and resources in otherwise useless flak frigates.