There are too many battles so I've never had enough patience to micromanage every little skirmish. Loosing a ship makes me angry and when all enemies are focused on one of your fighters you can't do anything about it.
I'm mostly relying on my mothership. My main tactic is:
1. pack ms with shield and armor reps.
2. keep fighters always inside ms
3. When battle starts, wait until most of enemies are focused on the ms and then launch your fighters and let them do the work safely. Do not make any groups/teams. Team members (except leader) fire less frequently (or don't fire at all) than when they are all alone.
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