The problem is... Capships are not designed to kill bombers. Bombers are designed to kill capital ships. If you start giving capital ships very effective anti-bomber weapons, we'll see Battleships mounting 10+ of them and hunting Light Fighters with them.
No, giving capships anti-bomber weapons is like arguing 'bombers can't kill light fighters effectively so lets give them better anti-fighter weapons!'
We had anti-fighter missiles last version. The result? QQQQQQQQQQQQQQQQQQQQQQQQQQQQ
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
"Incoming missile!"
You get the idea.
Capital ships are only a joke when you face them against Bombers. But have you ever considered that's exactly what it's supposed to be like? Capital ships are balanced to kill Gunboats and other Capital ships... not Bombers and Fighters. If you're sick of getting Bomber swarmed, don't fly your capital ship until the situation calls for it.
To me, the balance of bombers makes perfect sense. You want to load as much fire power onto a small machine as possible, have it able to fly in close range of this large, heavily armed death machine and kill it. How is a big, slow machine supposed to do that? It won't. That's why they're designed to be as light as possible...
The problem isn't Bomber vs Cap ship balance, it's Bomber vs Gunboat balance. Bombers should kill Crusiers+, Cruisers+ should kill Gunboats and Gunboats should kill Bombers.