Ships are largely static when in combat and face off nose to nose.  Why would they need side weapons?  Advent LongRange has side firing weapons -a counter to flankers, but only capitals and anti-fighter need 360 degree firing arc.

AA weapons on more than the dedicated anti-fighter eliminates their importance.  A Carrier Capital should probably have a AA weapon system to protect it from being focused by bombers rather than task its fighters for self defense.

You're absolutely right regarding Starbases. It's simply too big of a target to be able to destroy it without resorting to going toe-to-toe with it in some form.

Honestly, I'd say that starbases and cap ships should come with AA installed.

What I'd like, although the engine would need to be tweaked to allow this, is for banks to be on a per weapon basis, so that titan, starbase and capital AA would have it's damage per target nerfed to reasonable levels and doubled or more banks on AA only. That way it would not tear apart sieges, corvettes and LRMs as fast or faster than the main weapons, but could shred squadrons just as well. If my memory is wrong and multibank AA doesn't target individual fighters seperately, this wouldn't work.

As for making flak obsolete, the idea is that cap ships and up can protect themselves to an extent from strike craft, but that they aren't nearly as good at it for cost as flak frigates. Starbases should be incredibly hard to take out with just bombers through their flak and fighters, but not impossible.

As for anything else, ie heavy cruisers having AA, no just no. The lower-end ships are meant to be used in concert, and frankly anything below capital level that could target fighters would have to be so bad at as to be pointless or make flak obsolete by being able to cover itself and do something else also.

Because of how the shooting system is set up this can happen. The guns ae probably anti-light, that means it considers bombers, LRM's and scout frigates and non-TEC corvettes equal. In addittion the way shooting is set up, if it allready has the maximum number of bank targets engaged it will preffer to continue shooting at them than re-target somthing else, (like an enemy fighter or bomber). Lastly it's not just free damage. Whilst a touch weaker than the titans normal guns against heavy cruisers and support ships, it's twice as efective vs LRM's, Scouts, and non-TEC Corvettes. Lastly for TEC at leats it just looks dumb. Thos flak bursts really shouldn't damage the frigates at all, they're so diffuse they should just ping of the armour. It's like shooting a tank with a machine gun.

Add AA to all the battleships.  Then maybe the ones other then vasari one will actually get used.

I wouldnt necessarily agree that Battleships AA should be lesser then a frigate.  Take a modern day Battleship like the Missouri. those ships were loaded out with AA.  A ship that size should always have AA, space is no different.  AA is a necessity and not a maybe.

There's no game balance need for capship AA to be weaker than flak frigate AA on a per ship basis. Cap ships cost 5 to 10 times as much supply and have a command crew cost, after all. Even at say, 4x effectiveness per ship, either through damage, ROF, or bank, flak frigate will be far more cost-effective.

As for starbase AA, I think that should come either with the station, from a research subject, or as a part of the fortification or weapons line. Perhaps it would differ between factions? TEC gets them from a derivative of Hanger defense, advent gets it as part of rank one fortification upgrades, and the vasari station comes with it, given that it is meant to be used offensively and is liable to be under strike craft attack as soon as it is deployed?

Regarding the whole flak shouldn't work on ships thing, as best I can tell the TEC titans AA is the same as on their flak frigate, so unless you want to keep it from attacking ships, the titans flak guns should be able to.

Flak frigates may be more cost efficent, but even 1 flak frigate worth of anti-fighter firepower is still enough to largely nueter a single carrier cruiser. 4 frigates worth would be enough to shut down a carrier capital. Flak frigates are balanced by their reletive lack fo utility vs non-fighter units and their low focus fire potentiol. They do their anti-fighter job well but do littile else. A capital ship allready fills a multitude of roles.

Also Flak Frigates use the same weapons as heavy cruisers. Weatheror not somthing can fire at fighters is set in the individual weapons entry in the individual ship file. A similar tag for non fighters would go in the same place and allow/disallow shooting at non-fighters on a weapon by weapon basis. Weapon type and FX has nothing to do with what they can shoot at or how effective they are.

7DS took capitals and frigified them into battlecruisers, but it's too complicated to explain.  They are fun however.