One thing I like a lot about the Atlantis Bomber is the ability to put a pulse laser and a rocket launcher on it and still get adequate speed and protection. The pulse laser destroys the fighters and the rocket launcher destroys the ships. Or you could put two rocket launchers on them and have dedicated escorts to protect them. Also, the placement of the bombers on the deployment area makes a huge difference in battle. As long as you have 1 big swarm of bombers and not several small groups of them, they will do damage to the ship they are specifically targeting and the ships around it, basically destroying everything in range of their weapons, especially if the enemy ships have weak shields or armor(either should do). Normally the only thing constraining you is the amount of pilots you can have if you are just spamming bombers. You know, if you want to just goof off. Since pilot numbers are the only constraints, with a good sized fighter swarm you shoud get quite a bit of honor as well(if you succeed).
Me I just use fast missile cruisers with rocket fighter + painter fighters as escorts. Works vs everything I have ever faced when allowed.
Well except against those super heavy armored cruisers on that one map.
personally i like the faster fighters than teh ones with more firepower