One issue with the bomber's balance is that while there are several targets that are so dangerous that they require specialized approaches that approach is practically always "use bombers". Need to break a forcefield? Bombers. Fortress? Bombers. Spec ops post? Bombers. It used to be that spec ops posts required using missile frigates but at some point that balance was changed to require bombers (and then with the econ boost and damage inflation you could just throw a fleet blob at it even in the early game).
2. Frigates are much more suited for the "defensive" role. In other words, I think Frigates should be the counter to the "primary" Triangle ship, as their inherent attributes seem much more suited to that.
Back in 1.0 (maybe even as late as 2.0) frigates did counter bombers. But they shouldn't.
Yes, they're a defensive unit, but fighters have always always always been the counter to slower moving bombers. Check real world history.
I think that should have been fixed with a unit rename, not necessarily a re-balance. They were that way even in 3.0 IIRC. The game described that relationship as being natural, frigates being anti-armor, bombers armored and fighters fast to close in but knowing the game there were probably multipliers involved too. Frigate and bomber should have switched names, the bomber being a frail but powerful armor piercer and the frigate something heavy that excells in heavy hitting with the fighter maintaining the interceptor role and failing against the sheer firepower and armor of the heavy Frigate while ripping up the bombers.
When I was an RTS mod designer I often interacted with the Zero K team, they have a massive hate towards any form of multiplier. While I don't think multipliers should be completely removed it's still a better idea to use the natural properties of units for balancing rather than fairly arbitrary damage modifiers. Now granted, AI War uses significantly simpler combat rules than the Spring RTS engine but especially the armor mechanic the game has now that's pretty much laying fallow could have been used for an effective balance. Also the large engagement sizes should allow using overkill as a balancing mechanism.
I've never tried to balance more than a small handful of units though.