The issue has much to do with player philosophy and the Freelancer engine.
As to the latter - simply put the engine doesn't favour large ships - they can only fire at any one target at a time and if a player can't aim there is no facility for anything like, for example, x2 or x3 where turrets can be automated and perform generally well.
x3 is a good example, as egosoft changed the combat engine a great deal to create a situation where lone caps would be vulnerable to even one or two powerful fighters that remained out of range and could chip away at the large ship and dodge its fire. No longer did having a carrier or cruiser mean invulnerability - it certainly was a tough opponent, but it needed versatility in its load out and, most importantly, support ships.
In 4.85 I think the engine now favours co-operative play - that is to say, organised and eclectic fleets that work together.
Capships generally die first and soonest because they are biggest. And because of a habit that people have acquired in response to a particularly annoying way of behaving on the part of many players.
In furballs, in my experience, generally a cap turns up unannounced and uninvited, says narry a word (which considering the potential to RP a cap is pretty shameful) and opens up on all and sundry hoping to perform a Charles Bronson-like sweep of the nasty enemy as if they were so many mosquitos. In group chat someone says "target the cruiser" and everyone turns on it. It may take a while to down the shields and there are many other situations where caps live longer, but in the face of concentrated fire from several players, caps will fold up - and more importantly, they should. Call it truly democratic gameplay, if you want. Many players favour smaller, faster ships, just as many favour the larger, more cumbersome ships.
But it doesn't just stop at that. The idea that these ships should be invulnerable doesn't sit right with me. Why should they be so versatile that they can deal with any enemy? Why should enemy fighters and bombers not be capable of haranguing them and wearing them down - as it stands if you drift too close to a big ship, you are goosed. That is why balancing becomes so difficult: the philosophy behind all this. Why should the fact that someone has traded and earned millions of credits mean they can be placed in a ship that can easily dismiss all and sundry and force people to log off their characters with minimal regard to others. They have a place in the mod, certainly, but you can't have everything. And a misused cap has the potential to cause more annoyance than a misused light fighter.
Maybe we need more turret points mounting very fast firing anti fighter weapons that are energy efficient and have very fast projectile speeds are proper anti fighter weapons - but sacrifice range for damage - less than standard cap turrets - 8.33 refire and 300 damage would be conservative enough but deadly enough to deal with any small opponent within 1000k.
I like the mine idea, but not as a fighterght fighter fan. The days of buzzing between two caps and watching the pilots shoot each other as they tried to aim at me would be gone.
8 mines capable of dealing enough damage to instakill a fighter. Bad idea. Plenty of people would not favour any ship having instakill power. Oh wait, except maybe bombers... oh dear, what have I said...