OK - lets put flak on the caps. This would mean that like flak frigates, they can shoot down SC AND other ships. So you have just boosted the DPS per second of all caps. Have you considered the following:
What this will do when colonising. You will be able to do MORE damage to militia frigates while your primary weapons engage the primary target - e.g. kill the Garda/Cobalts quicker while focusing on the kodiaks. Is this a good idea?
Cap weapons increase as they level up. Keeping this in mind, what start out as 2-3 flak early game could quickly become 6-7 equivalent when the cap gets up to Lvls 8-10? Don't believe me? Look at the stats on a Lvl 10 Kol vs a level 1 one. 1 Lvl10 Kol will be able to take out 2 Lvl1 ones
Finally, you have removed the advantage that someone may gain by being bold and getting carriers early as they cannot get the numbers required to kill your cap. A person will just build LRM and fly under the cap's protection. This is just helping to bring back the LRM rushing from the early days. And if this happens, the flak isn't really required anymore is it? Kinda a catch 22. If you have it, people will change how they play = 1.05 carrier secnarios again. Currently I must make a CHOICE to get a Kol or Dunnov (assuming TEC) to get some anti-SC ability. The cost of this is not getting a coloniser cap or a Marza to experience up to Lvl6 quickly and early. Further, one of the ADVANTAGES a coloniser cap has is the SC they get at Lvl 1. Kol/Marza get them at 3-4. Its now useless if the other person's cap comes to the fight, whereas before it was only in danger if they had a cap with anti-SC abilities and/or carriers.
Good points, some thoughts
1 - Very valid concern, currently there is a toggle that determines if a weapon can hit strikecraft. The way to fix this problem would require switching it around if you want a weapon that hits strikecraft but not firgates.
2 - Honestly didn't even consider it, I think this is the first time it has been thought of in this thread. On the other hand, by the time a capital ships gets that strong there will be a lot more stirkecraft fighting.
Might want to add: 4 - the current engine only permits three weapons, adding a flak, fourth, weapon would require making a major change to it.
That aside, I think every good ship from fiction where there are strikecraft has flak of some kind. The problem is putting it into the game while balancing it to take into account your three points.
I think the best solution would be letting capital ships fire on strikecraft with their existing secondary weapons. This would keep current the current balance the same for frigates, cruisers, and capitals. Strikecraft should be the lowest priority for a capital to attack. A capital's levels could determine hit chance, base of around 25% and gaining 5-10% each level.
Real flak is probably something that we will have to wait for SINS 2 to get( Plus point defence/countermeasures for missiles)