Sucks, don't it? I'm already well vested in a Robotech plug with a capital/fighter scale weapon systems- and then I find the trademark weapons (the Main Gun, anyone?) can't be a beam. It just isn't right. The next best thing was a large, rotating energy ball that recursively sub-munitions itself when it hits things to promote the appearance of going through things. It works alright, but it just doesn't do the weapon justice.
Some notes to other people contemplating this type of system:
1. Balance is important. With planet-type capital ships, onboard fighters can be almost useless. I use them mostly as mobile point-defense systems, and battles look cool.
2. Fighters can't hit capitals, and capitals can't hit fighters. This is more important than it sounds. My solution is that the heavy missiles the capitals fire sub-munition into non-planetary light missiles, letting them hit both, eventually. The AI seems to have a little trouble with this, though, so be careful. Be sure to give your capitals a few point-defence guns to take out fighters. (All my fighters have the "can be hit by PD" flag on). But also, give at least some fighters a way to hit capitals in a pinch. One of my fighters carries bombs and a few heavy missiles for this purpose.
Done right, battles look very bitchin' done this way, with swarms of fighters shooting down missiles aimed at both themselves and the ships they are protecting, as well as the other fighters, and the capitals pounding away at eachother with the big guns. Again, be careful, as nothing is more annoying than to be rendered impotent, either way.
~Charlie Sibbach