Is it just me, or does this weapon seem overpowered?
Just one or two covering every part of my front line just annihilates all enemy fighters. Even against fighters that aren’t in formation, they are all annihilated before they even break apart.
I’ll admit to not being an expert, and have only been playing for a few months, but as a proposal for balance, how about reducing the armor penetration of the AOE part. That way, if a fighter at least has a minimal armor they can counter the AOE damage.
It is sightly overpowered if you preffer to use fighter-based tactics, but as you may have noticed the flak cannon damages anything inside its aoe. That means that you cannot use fighters to backup your fleet if you are using flak cannons.
If you are more familiarized with cruiser-based tactics, you will find flak cannons usefull to defend your cruisers and easy to ignore by your well protected cruisers.
In some ways it is OP, in others not. That depends of your point of view. If you ask me, i dont like them, they are fun to use but is hard to come with something good when talking about modding.
Even though you’re relatively new to the game, there’s no reason why you couldn’t create your own modded alternate of that weapon. Making the changes you described above is a trivially easy task.
Yes, the existing version of the Cruiser Flak Cannon is rather problematic, and in ways other than the armor penetration which you disliked. Big ways… The flak effect itself it set up in such a way that it seldom ever misses! 
That’s rather more than what I was hoping to see from its performance, and not in a good way. This function makes the stated tracking value of the weapon seem like pure fiction. I had hoped that the flak shell would create a blast such that even a near-miss would still inflict at least some damage to the target. That would have been nice, yes? But the pendulum has swung too far in that direction. I definitely did not hope for or expect a nearly guaranteed kill. That’s too strong.
Making your own tweaks is probably the best course for the foreseeable future. Cliffski is extremely busy with developing Positech’s next game, Gratuitous Tank Battles. GSB is not on his radar screen, and with good reason; he’s gotta pay the bills. The changes you propose might not happen for another six months, a year, or even never. Fortunately, weaponry specs are easily accessible to the player. I just wish that the flak targeting code was also a “user-servicable” part.