I'm probably going to catch some flak for this (pun not intended), but a good way to kill bomber and corvette spam would be to change them from Light armor to VeryLight armor, the same as fighters. I've never understood why fighters get VeryLight armor yet bombers and corvettes are as well-armored as full frigates.
Corvettes already have very light armor.
As for bombers: Do this and fighters lose much of their purpose. Fighters counter bombers entirely because bombers have light armor.
The current system, while not perfect, is much more interesting IMo then just having flak counter all strikecraft as hard as it does fighters.
That said, I'd love to see some late tier researches added to each race that buff fighters. Late game fighters fall more into the role of killing bombers the LRF anyway, which coincides with the late game being the stage wherein bombers swarms hit "critical mass". Honestly I thik it would be reasonable to add late game researches that either buff fighters or make capitalships more resistant to bombers.