I suddenly remember Carriers in Master of Orion (and - as someone else said - in pretty much every single Sci-Fi movie/game ever)...
As I notice in MOO3 (full patch no mod, at least), the Carrier pretty much dominates space battles due to its ability to sit back and let its fighters do all the fighting for it. Other ships just don't have the range, and so long as there's another type of fleet in there to serve as escort/distraction, the carriers won't fall and they just send out more fighters each battle. In Master of Orion 2, I remember the carrier design more as something akin to launching 'persistent missiles' ... the fighters flew in, faced point defence weapons (as PD is pretty much the only way capital ships can deal with fighters - larger ship-to-ship weapons just can't be maneuvered that quickly), dealt damage for a few turns, then returned for resupply before being launched again with a subsequent attack. I'm not entirely sure how well they performed in comparison to other vessels, as I tended to just have mixed fleets and didn't worry too much about what worked better than what. MOO3, however, makes it pretty damn clear as Long Range Armadas and Short Range Armadas start dropping like flies while the Carrier Armadas remain nearly untouched - SO LONG AS THEY HAVE SHIPS TO ESCORT THEM. This is the important point.
Homeworld - Bombers vs Battlecruiser. Ends in shame for the Battlecruiser unless it has ships with point-defence systems on them running escort (ie, Multi-Gun Corvettes or Assault Frigates, or even just the good ol' Interceptor).
Point is, Fighters can be countered with Point Defence. This is how it's supposed to be. Weapons downgraded to tiny, quick-to-aim/maneuver turrets/missiles can deal with fighter or missile threats, but can't deal substantial damage to capital ships. Large, overbearing weapons are great for anti-capital ship purposes, but can't hit the fightercraft that the carriers launched.
THIS is the balance of Fighter and Capital Ship combat. ACCURACY being factored in alongside a modular scaling of each weapon type. Not just saying Defence is all you need to avoid taking damage. Size and combat speed should be factors, as well. (Yes, I said combat speed, as opposed to just speed. I think there should be a distinction).
Also, all those saying the mechanics would be ruined... I already think they are with the damned Übertech. It's all ludicrous and, to be honest, it really intermingles near the end to the point where there technically shouldn't be a difference between the three damage types. Black Holes are Black Holes. They do one damage: Über. There's no Kinetic. There's no Explosive. It's just 'You are caught in a Black Hole and GRAVITY has now f**ked your a**'. I don't care if you have some ludicrous 'Zero-Point Armor' or a whole bunch of drones, PD guns, and ECM to protect you. You're getting screwed and there's no way out of it.
Anyone seen Farscape: The Peacekeeper Wars? Throwing Black Holes (or Destructive Wormholes) around is uberpower. There is no counter. There is no defence. There is only ruin and destruction. It frightened ALL races present to witness the demonstration into never trying to pursue such again. Even the evil Scarrans were convinced not to mess with it (though it did take losing most of their fleet and nearly losing their flagship to the Wormhole Weapon before they relented).