I've noticed that if I have flak frigates in just a numbered group, and tell the group to attack, say another capital ship, the flak frigates will move up to fire at the capital ship instead of at strike craft, and support vessels like robotics cruisers, guardians, etc. won't stay with the rest of the group, which essentially renders them useless.
With the ships set as a fleet, the flak ships only assault strike craft, guardians stay with the fleet, protecting it, and light carriers stick to the back where they're less likely to get destroyed. Seems pretty useful to me.