I prep for the worst across all bases. Some "standard" equipment for splash- damage, good melee-items, fire, shotguns and lots of dogs/ other aux units.
"Aggressive Retaliation" is not a good Mod to have installed and quickly inflates/deflates the difficulty. At first it's annoying but all the extra money out of the plasma-equipment quickly ramps up to a massive spike in power. The normal shedule of sentry/fighter crackdown approach can be entirely nullified once you can supply a fighter-craft that out-ranges the fighter /sentry.
Grey codex' conversion-launcher is one of the best solutions to boot. Outranges both ships and does enough damage to gun 'em down.
2x normal Seagull does it as well but you've to exchange fire now, causing downtime and costs more in the longrun.
Lancer-missiles are the "all-codex" alternative to the conversion launcher. Expensive but very reliable to do this specific job. Not the best damage potencial so no-go for big targets.
That's what the meteor-rockets are for. Once money is plenty, stockpile meteors in every base with a fighter in it and you can defeat almost every ship.