I know this might be hard to put in the game but what if you could board a ship with enough transports to capture the enemy ship. Kinnda like the Zann people capturing the Eclipse and the rebels from EaW that went into the imperial spacestation. Then you could get unique units for your own side.

Also to make it more realistic since the ship wouldn't have the right crew it could only do half damage (like when using engine boost).

Don't mock me for this because I can dream can't I?