Taking down fully recharged shields every five minutes is exhausting, and more importantly, stops you hitting those juicy subsystems. Generally, you’ll want to take out the shield generators first.
The shield generators (unsurprisingly) power the capital ships’ shields, and recharge them once they’ve been depleted, the targeting systems improve the accuracy of the AI turrets, and the power system overloads once destroyed, leaving the hull riddled with weak spots that can be destroyed for additional damage.
