More bombers.
Again I might be showing my noob stripes, but I kind of don't mind this. "Oh these nuts are kinda tough to crack? Send in the marines."
I'd like to again point out the distribution of things that the bomber kills:
Structures (guard posts, which are every where, force fields, which are everywhere)
Fortresses (which murder everything but bombers, and bombers have a damage multiplier)
Hybrids (which the AI builds in multiples of 137)
Golems (exogalactic waves)
Avenger (obvious)
Hunter killers (which I've yet to see, but they sound relatively common for the late game)
Command stations (which you tend to want dead)
Some guardians
about third of all fleet ships*
most starships*
Compared to what fighters are good against:
Bombers
Some guardians
about a sixth of all fleet ships*
Or what frigates are good against:
fighters
some guardians
a handfull of low-hp fleet ships (swarmers)*
There's not even a problem of "well duh you get more of the right unit" it's a problem of "the right unit is ALWAYS the bomber."
*Made up values. I don't feel like looking through the entire list of some 300 different units to figure this out.