Some one mentioned in this thread about boosting the bomber thrust speed (250-275?) for bomber runs (probably make specialized thrusters with limited energy) so when they make their run they're not absolutely sitting ducks against pursuers. But (and I stress you to consider this) when they have to turn around for another attack/recharge their thrusters, the fighter can take advantage. Granted the agility of these craft are snipped slightly.
Another point I tried to get out somewhere was about making a line of bomber guns/turrets with awful speed but extreme projectile range along with moderate damage/fire rate and energy consumption. This way bombers wouldn't be so often abused to bravely PvP fighters. We could also look into adding more torpedo slots (3-4?) and expanding the array of torpedoes/anti-capship weapons (emp torpedoes/bomber class pulse cannons and finally hull busting torps).
I also thought of possibly making very heavy "dept charges" for bombers with damage maybe 1/3 or 1/2 of the hull busting torpedoes just to make the bomber runs more interesting, of course probably knack the refire rate some, boost up the energy consumption (mines do/can be made to consume energy right?) so their not used by fighters, and of course, reduce their speed so they don't easily track and destroy fighters (unless they're stupid enough to get caught in it's blast radius.)
Then theirs the armor well in combination with the two above, the armor might be able to be left alone. The shielding could be bumped up again to freighter class just so they're aren't completely helpless against fighters and attackers despite the agility nerfing.