my idea, just discussed with dusty in-game, was to remove ALL guns from bombers, give them a couple more torpedo slots, and add a variety of torpedoes to the game (and remove the supernova cannon altogether).
For example, shieldbuster (emp) torpedoes, dumb-fire torpedoes with a larger blast radius and heavier warhead, cluster torpedoes, etc.
This would make bombers near useless against fighters (how many fighters have you managed to kill with a nova torp and nothing else?), but keep them effective against caps.
It would also allow us to rebalance fighter guns for higher projectile speeds, to make them more effective escorts and shorten fighter furballs, since bombers would no longer factor into gun balancing.