I see anticap cruisers as essentailly one big gun- not too powerful on their own, but put half a dozen together and pit them against anything. You really can't just beef up the weapons on a cruiser, they're smaller and weaker for a reason, and it ruins the balance of a game. Try it sometime- something like a Mjolnir with engines and thicker armor- they're great if they're none too fast as well, since they spend most of their attention on the gun, just specialty ships built for heavy fleet coverage... you could also have a midrange vessel, basically a small corvette (That's what corvettes are, Shrike) with some light anticap and some relatively vicious antifighter weaponry...
How 'bout something like a remote-controlled Argo loaded down with high explosives- basically a really, really big missile that acts as a capship in the game? You can send it into a swarm of fighters, and when they blow it up (it would have to be rather weak, what with the unstable explosives), it lets out a shockwave killing much of the enemy fleet. Wanna nail a heavy capship? Just get it close enough and ram it into the thing! This seems to be the way the GTVA is heading anyway after FS2, with all the kamikaze Orions, etc.