Admittedly I normally play through on easy and have only been playing for a couple weeks.
However my entire strategy usually hinges on taking out the guns first. Most time I can roll all but the toughest foes or the ones who get a missile off before I can charge my first volley. Most fights turn into five minute nearly risk free waiting games.
In fact, when I found a weapon pre-igniter I got my keeping them down achievement the very next fight, it took a while to grind them down but they never successfully fired their weapon.
Sometimes I need to rocket their shields, or target their shields when the weapons are already down, but I have not had luck targeting anything but the weapon systems.
Is there a better strategy?