You can't bandbox target things in this game afaik (although I wish it were so), so pausing is pretty much necessary to focus fire on something moving. The list right now is:
zombie guardians > emp g > self-destruct g > laser g > hybrids > tractor g > flak g > all other g > bombers (if necessary to set a preferred target while defending against a wave) > etherjets or other tractor ships (because they always drag my ships through wormholes and aggro new stuff on the far side) > guard posts.
So that's a lot of pausing! I also pause a lot when I'm considering strategy, or when I'm placing a lot of turrets or building shields or doing other time-critical stuff. Probably spend at least half the game paused.
But I mostly play singleplayer. I think I could be broken of a lot of my pausing habits in multi, but not all of them. Sorry, whoever plays with me!