The main thing I see here is the fact that the Aeolus has not enough blob turrets. Believe it or not, blobs are the main defense against bombs, not flak. All the times I played those missions, none of the bombs were destroyed. Why? Flak sucks
.
Now, play the first mission again, but replace the Aeolus with Leviathan (and change its name just for good measure
). The Leviathan has four Anti-Fighter beams, whereas the Aeolus has only two. 3/3 times the Leviathan dies, but, usually 2/4 of 'Attack' wing is destroyed. Anti-Fighter beams are much more dangerous than Flak, and take down more bombs. So the Aeolus may seem more fearsome because your screen is always pulsing red, but the Leviathan is more dangerous.
Next, change it to Lilith. I see, 3/3 times the Lilith is destroyed, and the damage to 'Attack' wing is very light (most damage is done by the single SAAA gun anyway). However, it takes down quite a few bombs, but not as many as the Leviathan. This is proof that Flak guns hit bombs 1/10 times, but blob turrets are far more accurate and usually hit bombs. However, blob turrets do next to no damage to bombers or fighters.
Conclusion:
Flak Guns - Flak guns are okay against fighters/bombers but can't hit bombs.
Blob Turrets - USELESS against fighters but good against bombs.
Anti-Fighter Beams - Good against both fighters and bombs.
Wait a sec, how'd this get so off topic?