Credit - You are making things up again, picking things to support your argument without using the whole scenario you are lifting them from. You talk about real life and then base it on WWII.
In real life, the battleship - the epitome of what is considered a "capital ship" - is literally a moving Flak platform on wheels. The largest battleship ever created had over 150 Type 96 25mm cannons, and over 25 type 93 13mm triple AA machine guns, other ships indeed almost any ship worth anything in battle carried Flak guns. Naval battles in the pacific tended to be massive Flak vs. Strike Craft contests with a lot of puff puff clouds covering the sky for miles.
What is this battleship? Which fleet is it currently serving in? Battleships are now obsolete in their traditional role. Now the are more for shore bombardment etc...
Today a carrier is the major ship in a fleet. They are surrounder by destroyers and cruisers that provide protection. However their main defence against enemy fighters/bombers (or even interceptors if someone was to use them) are their own fighters etc...
Why? Because they can fly over the horizon. The idea is to kill something BEFORE it can fire its weapons. By having an AWACS up, they can vector something to fly towards the attacker and engage it long before the carrier has it on its radar. In fact, the carrier's one is probably off due to it giving away their position.
The weapons on the carrier itself is point defence for last minute targetting of missiles that are close range - i.e. a few miles away or less.
In any canon Star Wars hand-book of ships, it lists major capital ships such as Star Destroyer as carrying several AA-missile batteries and AA-Ion cannons in addition to its TIE squadrons for a secondary line of Anti-SC defense.
And it was an A-Wing that took out the Executor. It's "flak" didn't protect it. Also, according to canow the Empire built the Lancer FRIGATE to kill the rebel fighters. The rebels fielded a Corillian Gunboat for a similar role.
In the B5 universe, those guns you point out are often used to shoot down incoming ordiance as well as fighters (That's what the star furies are used for).
Interceptors of both types were used to defend against incoming fire, as well as shooting down enemy starfighters. They fire slow moving pulses that actually intercept and disrupt incoming fire. The nature of this effect is unknown. It is also unknown how many interceptor emplacements are present, but they appear to be well positioned, allowing good coverage of the sky surrounding the station. In the image above right, the new interceptor emplacement is located off the starboard side of the communications tower (seen in the background).
THIS IS FROM THE SAME SITE
Now to be fair, they DID say the following about the bottom left grid gun
This emplacement has 4 barrels, each of which fires short blue pulses at a high rate. Reminiscent of a machinegun, this battery fires each barrel separately 0.17 second apart. This weapon is used against both starfighters and large warships.
They also pointed out that the defence grid overheated fighting a Centuari ship.
Babylon 5's defenses began intercepting Centauri fire at approximately 7 seconds into the clip. The announcement was made that the interceptors were overheating at approximately 21 seconds. Assuming that the battle is presented in realtime, B5's interceptors can defend the station from a Centauri warship of this class for less than 20 seconds, even though the warship was firing at multiple targets outside of Babylon 5.
Moving onto the game itself.
For those complaining about the lack of flak on star bases - BUILD SOME HANGERS. Outfit them with fighters and get the upgrade for flak for them. You now have flak surrounding your starbase. Which is actually better as it start hitting ships before they get to you if you put them in front. Plus your fighters will have started thinning out the enemy SC.
What I propose is: give all capital-ships a general weak Flak capability equal to 2-3 Flak Frigates.
Why not just build those 2-3 ships. They are a level 2-3 tech and don't cost that much???
Some Capital Ships have two thing to try to deal with SC, but with 1 they fail completely, the other is very micro/anti-matter dependent. I'm talking about of course their own SC, and their own capitial ship abilities that some ships have. The flaw in the first one is that the number of squadrons a cap carries (1-3 max) will almost never be enough to really protect it against enemy swarms. Second, the abilities are anti-matter dependent and highly situational. None of these 2 give a good reason why capitals shouldn't have a reliable built in Flak both in game-terms and philosophically.
Lets see if I can find the FLAW here. You talk about an enemy swarm. Lets give it an arbitary value, say someone with 10 carriers vs 1 cap ship. Apart from the differences in fleet supply and ship cost, there is no difference between the two. So yeah. This is a valid argument. Forget I said anything. Please continue.
No wait - lets look at that some more... Come on, be serious - NO capital ship goes into combat unacompanied except for in the early game when you have scouted and know what you are facing. You don't send a Lvl1 cap to colonise a terran with 3 kodiaks, 4 garda, 5 cobalts, 3 LRM and some krosovs either. And if their SC are hitting your cap then they are either bombers which your SC will kill quickly, or fighters which do less damage and your SC can thin them out (since these are what most people build and swarm).
Here's an idea to help protect your cap - get some Hoshikos/ceilos (or overseers/subjugaters + guardians) to help repair them. Or maybe a second cap with an anti-SC ability so you get some synergies going???
"Capital Ships aren't supposed to be a one-ship fleet, they support, and need support... they need Flak Frigates ad fighters already with them. Capital Ships are limited by hardcoding to three weapons systems..."
They're not. Capital ships will still very much need support to be effective. Giving capital ships a weak Flak will not by any means make them one-ship conquer all wonders. Flak Frigate support will still be very much desired, Fighter support will still be very viable. As for hardcoding, there are mods out there that already has this as a feature, so we know its all very much possible.
So by your own acknowledgement a cap cannot stand on its own... Cool. You just defeated your own agument. Good good. Enough SC hitting a cap without support will kill it!!! Genius at work here.
If you had a suitably balanced fleet with a similar number of points spent, the cap will still go down to frigate focus fire unless you micro it. Or your SC will kill THEIR cap and they have the same complaint you have. Except you will be happy as you won!!!
Also - when talking about how people have modified the game, you didn't ask "What have the mods changed to achieve this flak ability"? There are many mods out there that many people feel would ruin MP games, but are fine vs AI. For example, one of them is a version of Go-Big or Go-Home.