hold on guys, I'm modding the game a bit to make the flagships have more hp shield and armor bonuses, and modding a pd module so that it's actually effective.
Ok, game modding maintenance and upgrades complete. Your flagships now have a hefty 50% bonus to health, armor, and shields. Also, there is a new ship you'll all be getting, it's a big ugly point-defense rabbit cruiser. Should be able to shoot down about half of the incoming missiles from missile blocks. Still can't hit plasma torps though.