I was thinking on the whole Bomber debate for a while, and I had a thought. Would this sort of idea work?
First of all, give bombers a big shield. Something like 100k, but with the caveat that it was of a different variety than every other type of fighter shield. And only bombers could equip it.
Now, this seems a big boost, but the thing about this new variety of shield (made from some exotic sounding particles, just like the others, eg graviton) is that all of the standard technologies would blast it good. Tachyon, neutron, particle, plasma, laser, photon, and pulse guns would all do about 500% damage to this shield. Ouch! This would make it, in practical terms, 20k for any fighter. Transports and capital ships, though, have weapons that aren't of a particular type, thus they wouldn't get a bonus, right?
Then to make up for this, lower the armor of bombers significantly. For the Roc, for instance, perhaps make it 4000. That makes it 10k with a Mk VIII armor.
In the end, then, bombers would be pretty well defended against capships, but be much easier for fighters to pick off. Perhaps not those exact numbers, but that sort of idea. Basically make them giant, mobile power plants, throwing off supernovae and generating a huge shield, but not having much armor due to most of their composition being power generators of sorts.