I think a better solution would be to stagger out Exo waves a bit. The botnet alone is worth an exo wave (and it usually chews through them fast), but the other golems and spirecraft aren't generally strong enough in a straight up fight to justify doubling that exo wave size. This runs contrary to the purpose of those craft being needed to counter the exo waves; instead of using golems and spirecraft vs exos you use them to cleave a path through the regular AI ships then when an Exo wave comes you hide them in a corner because they are irreplaceable and die in a blink of an eye.
Seeing how Botnet Golems essentially let you have infinity units given enough patience I have a hard time believing the counter can be too strong though. It's just that Botnet + Golems + Spirecraft + normal forces are not nearly able to fend off 3x as big of an exo wave as Botnet + normal forces alone, more like 1.5x. If the 2nd exo started just as the first was ending, and the third just as the second was ending, the difficulty would scale closer to the actual player strength.
I'm also for customized waves for each type of exo wave. Whether the waves should be tailored to counter or be countered by the Botnet/Golem/Spirecraft is up for debate. Of course, if the botnet is supposed to beat botnet waves then by corollary all other waves should be immune to reclamation