I suggest the following:
1. For consistency, EVERYTHING that is poison should deal damage (poison type) AND ability damage (as per the actual rules of the game. You know, those things you ignore these days?). Spells, weapons, natural attacks, traps, etc.
2. Add POISON RESISTANCE as a form of energy resistance. This would act just like any other ER against the HP damage of poison attacks.
3. Restore POISON IMMUNITY or change Proof Against Poison as follows: Poison Immunity would negate the ability score damage from poison while leaving the HP damage intact. Or change Proof Against Poison to where the bonus (i.e., PAP +6) acts as DR against the ability score damage. For example, PAP +6 would negate 6 points of ability damage from a poison attack. Note that's total, not per saving throw. So you might still take damage if you fail the secondary save.
4. Add NATURAL POISONS to the game. As it stands, PAP is supposed to make you immune to natural poisons. It does not do that. Or it does, and you've just changed everything with a poison attack to make it a magical poison (which is some bogus ****).
5. Add POISONS FOR WEAPONS. These should be available to buy in some shops, and craftable by Assassins, Druids, and Artificers. One "dose" could add poison damage to a weapon for x amount of time or x number of successful hits.
6. Do all of the above to diseases as well.