The fire at will button helps a lot, what I do is select fire at will and look out for enemy ships being destroyed, every time the enemy fleet is destroyed I press fire at will to reacquire targets. If I want something specific shot at during a large battle I tend to only want specific ships to change their targeting anyways and not the whole fleet so it's not total agony.
That being said with missiles this still works but not as well, it's mostly for beam melees.