Add Fleet battles where you fly a ship of choice, whether you are flying a nimble fighter craft, or a command ship. You seek out the other person to duel them, a victory against them would add a percentage victory modifier to their fleet, and vice versa for a loss. You could choose to use your superior flight skills to fight their fleet, and ignore the enemy dueler, at a risk of weakening yourself when they do eventually find you. (Trade off, less fleet ships, but weaker versus opponent.

Anyhow, dueling while the fleet battle handles itself normally, or even with a small AI coordination with you at a low programming complexity.