Each battle when you have a mix of large and small ships, they appear in a spread out formation. For each substantial battle, I advance my large ships which have the most shields, armor and missile defenses. Then pull my small ships in behind them. No use to hit the auto-combat button which will put my small ships way out front, get them focused and destroyed.
With this latest update in testing, the AI will sensibly flee battle if you have them out gunned. It would be a big improvement if its immediately visible when any enemy ship is set to flee. I don't know how many times I've individually moved 20 or 30 ships to a more sensible formation and next turn the AI flees. Its aggravating.
The AI might battle, forces are possibly somewhat close. Move 20+ ships. AI flees. Repeat. Thinking about it, why let us enter the battle screen at all? If the AI can pull out with no losses. Use the auto-combat results to determine if its worthwhile to give us the option to battle.