I'm statting some NPC/Monsters with class levels (so PCGen comes into its own).
They have Bite attacks (Serpentfolk). Bite on its own is a Primary attack (full BAB, full Str bonus).
However, being busy little warriors, they use weapons - and by the rules that demotes all natural attacks to Secondary:
"You can make attacks with natural weapons in combination with attacks made with a melee weapon and unarmed strikes, so long as a different limb is used for each attack. For example, you cannot make a claw attack and also use that hand to make attacks with a longsword. When you make additional attacks in this way, all of your natural attacks are treated as secondary natural attacks, using your base attack bonus minus 5 and adding only 1/2 of your Strength modifier on damage rolls. Feats such as Two-Weapon Fighting and Multiattack can reduce these penalties."
PCGen default adds and equips "Bite (Natural/Primary)" but doesn't offer a chance to add a Bite-as-Secondary, nor to have a way to demote the stats of a Natrual attack (bite) when used with Weapon.
I would like any one of
a Temporary Effects option "Natural Attacks demoted to Secondary" to demote all equipped Primaries to Secondary.
**User should add when statting character with mixed attacks.
lack of this is as current. (Assumes you use a subset of your "best" attacks, and skip the rest?
option in the Equip menu for Equip to "Secondary attack".
Default Equip would be as per current rules (Primary for those listed as such, Secondary for those listed as such in the Bestiary)
don't offer the alternative Equip to for those already Secondary in the Bestiary
An alternative, even more wonderful solution, would be to add a generic Natural Attack to the Weapon chooser, to let you build options with the Custom weapon menus, Primary and Secondary being alternatives to add to the weapon, along with damage dice.
That's also be a neat way to handle some of the more complex spell and supernatural bonuses where you can add Elemental (e.g. Fire) damage to a limited number of attacks (e.g. 1 claw, out of 2 or 4). When you have more than one of these, the current system breaks down completely. This would let you build a "Left claw(fire)" and "Right Claw(shock)" character.
Pathfinder Core Rules