Part of the issue with Puffy vs. Fighters vs. Bombers, is how it's generated.
Puffy ack is not actually fired by the gun positions like the manned and auto guns are. Puffy ack is generated automatically in a box around the target (this is why puffy ack can shoot through mountains at targets with no line of sight). The reason it's more effective against fighters is that the AMOUNT of puffy ack remains the same, but the size of the bounding box around the target stays smaller. Thus, fighters fly through a MUCH denser amount of ack than a bomber formation with its larger bounding box.
The solutions would be to:
1) Decrease the concentration of ack along with the size of the ack box.
2) Keep the ack box the same size regardless of the type of aircraft
3) Rather than targeting one particular aircraft or formation, make the ack box one large global blanket around the ENTIRE task group.
4) Rework puffy ack entirely so that it's actually fired by the guns, rather than generated around the plane (IMO this is the best and most realistic solution).