Patch 2 gave both defenses real resistances: armor favours kinetic (24% kinetic, 20% high-explosive, and modules can't push high-explosive higher), while shields now start at 10% kinetic and 30% high-explosive, with high-explosive modifiers in the shield pools.
So armor counters turrets and shields counter missiles and mines. Are you running one, both, or switching depending on where you fly? Share what's working.
Related answers: What are the damage types?, Are resistance bonuses worth it?