I've talked about countering absolutes (like Tumble saying you don't provoke AoOs and Thicket of Blades saying you always do) and possible changes to the system to resolve them before. Now, I'd like to talk about a specific subset of that, immunities.
Immunities: Each immunity has a strength, a numerical value of 1 or greater. You're effectively immune to anything for which you have an immunity strength of at least 1. Having an immunity strength greater than 1 doesn't do anything in and of itself, except when interacting with pierce. Multiple different effects that grant immunity of the same type stack their strength values. Immunities of different types that apply to different effects of the same attack don't stack their strength values; evaluate each one independently to determine what effects of the attack are prevented.
Pierce: Some forms of attack have a pierce strength, a numerical value of 1 or greater. Most attacks don't have a pierce strength (treat them as 0 where relevant). Pierce doesn't do anything in and of itself, except when interacting with immunities. Some forms of pierce only function against specific types of immunities, rather than any and all immunities.
Resistances: Resistances are like a lesser form of immunity. They count as immunity 1 against damage sources that match their damage type, but only apply against a certain amount of damage from each source, as indicated by the resistance. Some resistances count as stronger strengths of immunity, as noted after a slash (similar to damage reduction's notation). For example, fire resistance 30/2 counts as fire immunity 2 against the first 30 points of fire damage from each attack. Resistance strengths stack normally as per and with immunity strengths with regards to the points of damage that they protect against (including with other resistances of the same type). However, the quantity of damage that resistance applies against does not increase with multiple sources of resistance. For example, a creature with cold resistance 10/1 and cold resistance 10/3 is equivalent to a creature with cold resistance 10/4, and a creature with sonic resistance 5/1, sonic resistance 20/1, and sonic immunity 1 effectively has sonic immunity 3 against the first 5 points of sonic damage, immunity 2 against the next 15 points of damage, and immunity 1 against any remaining sonic damage and non-damaging sonic effects.
Immunities vs. Pierce: There are two ways I can think of for this to work. The simple way, in which you just subtract one from the other, would leave you with an immunity if you had more immunity than pierce, or no immunity if the pierce was greater than or equal to the immunity. Optionally, equal amounts could have a 50% chance of counting as immune to non-damaging effects and reduce damage by 50%.
The other way is a bit more complex. Rather than being all or nothing, it would be proportional. A creature with immunity would have a (immunity/(immunity + pierce)) chance of being unaffected by non-damaging effects (damage being reduced by the same fraction), and a (pierce/(immunity + pierce)) chance of being affected normally by non-damaging effects (taking the same fraction of damage). For example, a creature with immunity 2 being attacked by by a spell with pierce 1 would take only 1/2 of normal damage and would have a 1/3 chance of being affected by non-damaging effects.
Most mechanics of immunity can remain relatively unchanged, granting immunity 1, with the exception of energy-based subtypes (fire, cold, etc.), which should grant immunity 2. The few mechanics that allow attacks and effects to bypass immunities can be changed to grant pierce 1 (if the immune subject is still granted a substantial defensive benefit) or pierce 2 (if the immunity is completely negated).
Below are some examples of effects that can be altered and simplified due to the changes above.
Piercing Cold [Metamagic]
Benefits: You can only apply this metamagic feat to spells with the cold descriptor. Piercing cold spells are so horribly cold that they are capable of damaging creatures normally unharmed by or resistant to cold. Piercing cold spells gain pierce cold 1. Creatures with the fire subtype who are damaged by a piercing cold spell take double normal damage instead of the usual +50%. A piercing cold spell uses up a spell slot one level higher than the spell's actual level.
Truedeath Crystal, Greater: As the lesser crystal, and attacks with the weapon gain critical pierce 2 against undead.