1st, have their standard weapons do minimal direct damage, but have damage over time(DoT), to give the feel of the enemies ships being eaten away by bio-plasma. I can see it possibly being a problem though if hte infobox gets filled with miniscule DoT lines, so possibly make the ships' DoT effects cumulative, so you end up with a single large value rather than lots of little ones.
This is a problem I've been considering recently. The current theme of weapon damage 5% upgrades is something I initially modded but have found to be boring. I've been leaning towards a purely ability based upgrades on weapons to make it more interesting. This idea fits nicely with what I have been considering.
2nd, Instead of fighters and bombers, i was thinking it would be cool to have only bombers, and have them suicide onto enemy ships. small squadrons and low health, but rapid build time. Just to keep things fresh! again, there is a downside i've already thoguht of, they would need a different weapon class to usual so that they are effective against LRM spam. To make up for the lack of fightes on the defensive, i was thinking have the flak frigates have no guns, but a damage over time aura, to compensate for the lack of fighter support. That aura would have to replace rather than stack though, to prevent a small clump of flak frigates being untouchable by fighters or bombers.
The bomber is a good idea. I think there is a way to balance this out with like stated with rapid build times. Removing fighters is riskier though as bombers are pretty OP in the game currently. There would need to be a way to deal with bomber based fleets (i.e. a counter would still be needed). Your idea of the flak frigate is very interesting, my concern is it would have to function as the fighter counter and the bomber counter.
I'm actually wonderg if the same concept for bombers can be done for fighters and make the whole thing kamazi attacks.
I like the ideas and I'll mull them over to see how they could be implemented with balance in mind.
p.s. if I even come close to using either of these ideas I will include your name as a resource on this mod.