Feedback of video, (tactics wise)
To hell with the sensor relays, the enemy can have them. Cap the communication dishes and the nav points. The pathetic muzzle valocity of the enemy ships makes any range bonus they get a laughable bonus, (please: shoot from farther away, so I have an easier time dodging)
Having the speed bonus is paramount for your flagship, you rush up and around the onslaught and lay down the broadside guns onto their side. Or preferably: their aft. Do it at point blank range, there's no sense in being timid and risking wasted shots.
The commrelays give you the numbers advantage. Which is also nice.
What are you doing deploying the flagship immediately? Deploy the point defense frigates and heavy fighters, take the above mentioned objectives with a vengence. Any other ships can chase down the enemy. Your flagship should be delayed, (if not deployed last) until some of the enemy bombers are destroyed.
When flying the flagship, you suffered heavy damage to your starboard side. Although, yes this is bad. You made the mistake of keeping that side available to the enemy to shoot at. When the armor fails: rotate, and show the port side, instead, to the enemy. Also, you keep your shields up too much. Anything that drains energy, prevents you from firing all your guns at maximum efficiency. If you can destroy the enemy in 10 seconds, why bother taking 30? It allows them to fire upon your shields longer, increases your flux and causes you to overload. Taking a missile salvo from a long range fire support vessel. If you out gun the enemy, just annilate them in the fastest manner possible and move on.
Lastly, if you get bored waiting to pilot your flagship, swap command in the command overlay to a different ship, and have fun.