I'm damn sure this has been suggested before, and it's definitely not my idea, but I'd like to bring it up again.
Please let me tell my ships to avoid certain enemies. I've lost too many ships because my ADD captains decide to get distracted from their orders and go poke at the Onslaught with their little machine guns. I'll deal with that big scary capital when I'm good and ready, not when my captains decide it's time.
Or even let them avoid each other. I want to be able to use my big guns without little frigates flitting around past me when I'm dueling a capital they can't handle. Then they get killed. Sometimes they plant themselves in front of my tachyon lance support.