From my understanding, the core of the problem is in strikecrafts -fighters- themselves rather than whether we have to put some good flaks on capitals and starbases. And putting flaks on capitals rises another concern that it may devalue some capital's anti-strikecraft abilities (i.e Kol) but maybe it won't be problem anyway.
No misunderstanding, many people recognize the problem. Look at Strategy and Multiplayer sections. The key problem is that strikecrafts are virtually free that flaks and anti-strikecraft technology are very ineffective regarding this issue (since they don't make carrier owners cost anything)
Instead of putting flaks on every single big objects, the whole carrier mechanics need to be changed (and it is currently on discussion on, again, Strategy and Multiplayer sections) to fix this problem.
BUT, if Ironclad won't fix strikecrafts, then flaks are indeed good addon for capitals and starbases; the current situation is almost beyond control, and while flaks won't help that much, it is still better than having none.
Again, maybe some flaks won't be helpful for your capital ships, chased by 50 fighter squadrons, but it is still nice to have flaks.
Also, you must realize that bombers appear rarely, due to massive number of fighters being created in games. This is because there are very few things that can kill fighters, which are fighters themselves and flaks (with exception of abilities) If capitals and starbases, or other big objects can surpress fighters, there would be more oppounities for bombers to be used.
From my understanding for game balance, it is essential to have counters to specific unit in RTS, and in this case, flak is only -supposed to be- counters to fighters.
Now, ask any experienced players whether flaks are good for fighters. The answer would be no; once I saw a player with 35 flaks try to counter 25 vasari carriers full of fighters.
...He could get situation under control only after his hw and some planets completely wiped out. See, flaks are not working properly and there may need for some more firepower.
At last, even though a starbase can have a maxium of 20 fighters, and hangers can have more squads, they are still not enough for typical carrier spam. I mean the number of carriers I usually see is more than 40, total of 80 fighters...
....you are not going to defend against them with 40 or less fighters. You need some more assistance.
So, let's wrap up.
1.) In current state fighters are too strong; they need more supress fire from more units.
2.) More flak-present environment allows us to use bombers, aiming for diversed tactics.
3.) In current state of balance, it is not possible to defend worlds with only fighters provided from hangers and starbases.
4.) Flak frigates themselves are not enough. (maybe this looks like duplication of no.1 But this is very different issue. Ask me if this needs more explanation.)
5.) All of reasons above are not applied and not necessary if Ironclad fixes strikecrafts, completely eliminating the core of the problem.
P.S : See, without that smile, the whole paragraph looks more serious and professional. And I really appreciate your decision to not put smile for my post.