I think bombers aren't too good, rather the players will often realise in a certain situation that they need bombers - this rarely occurs for the other types.
Also I'd rather overhaul the armour/hull combo at the same time, which I see as a higher priority.
One set of potential changes that try to preserve the triangle relationship:
- Change the relative caps to 6:2:1 Fighters:Bombers:Frigates.
- Give Frigates AoE, i.e. turn them into Grenade Launchers, and mitigate their AoE immunity into resistance.
- Alter mechanics like targeting priorities to enable fighters to screen friendly untis of the same size (i.e. bombers).
- Reduce the omni-presence of shields, and/or make it such that, e.g., shields cannot protect units from enemies inside the bubble (thus giving them pure anti-siege roles).
- Change the AI deployment to favour bombers less. Say, some Guardposts are defended by large fighter complements (encouraging frigate use). Reduce the number of shots of anti-fighter/bomber guardposts, but make them accurate/damaging enough to OHKO those light units (encouraging fighter screening).