Flaks use up too much energy imo, you can use Missiles and Mortars more than you can flaks.
Hows about.... Take a Mine Launcher, the mine it launches being basically a blue translucent shell that covers the entire ship (for Battleships). Itd basically be an emergency shield. 50k hp, 5 second life time, 15-30 second cooldown.
And on the subject of anti-cap weapons..... Something that IGNORES shields perhaps?