We're doing much the same really. Capital ships of similar sizes are very effective against each other, but less so against fighters. That said, Battlestars in particular have some nasty anti-fighter tricks up their sleeve as well as a very impressive flak barrage that you *have* to avoid if you want to attack them, though this has limited coverage. On the flipside, Basestars are almost defenseless without their legions of Raiders, but pack some extremely powerful ship-to-ship missiles that let them decimate enemy warships at a distance.
I'd say that up close a Battlestar has a clear edge over a Basestar as the combination of its flak barrage and main batteries will simply tear it apart, but at long ranges it's the other way around. Larger Battlestars such as the Mercury class might fare better at long ranges, though, due to their main battery firepower being able to match that of the Basestars.
As for fighters, they are very important in all engagements but, unless they are equipped with nukes, are not ideally suited to the task of actually destroying Battlestar-sized targets. Fighter guns do very little damage to Battlestar-level ship armour. However, even without nukes they can make a critical difference by intercepting warheads, taking out important turrets/subsystems, preventing the enemy fighters from doing the same, or even taking out smaller supporting warships that aren't as thick skinned as a Battlestar.