3d6 said:
Second, I would change the rules so that stacking rules only apply within their own class of effects. For example, two magical items providing a deflection bonus to AC would not stack, as they are both magical items. However, a magical item and a spell providing a deflection bonus would stack, as they are different classes of effect (magical item and spell). This would mean that you would only need to check magic item stacking when you change your magic items, not every time a spell was cast upon you, and you would only need to check spell stacking when you had more than one spell effect in place.
Why have named bonuses at all then? Only allow classes of object to provide bonuses: Armor bonus classes: Dex, class feature, armor, shield, all other items, spells. If you have bracers of protection and ring of protection, only one applies. You could even say Dex, class, shield, spells and all other items. So that Armor (magical or not) doesn't stack with bracers.
You can generalize this to One Ability Modifier, One Class Feature, One Spell, One Item and One Exemption Item *. The exemption item only applies to attacks and AC (unless you can figure out what the exempt item is for spell resistance, saving throws, and skill checks):
For Attack Bonus and damage, weapons are the exemption item
For AC, shields is the exemption item
Note, it says item, not magic item. Thus you can extend the masterwork rules to allow for amazing mastercraft items and they still work within the framework. Also in this system physical armor does not stack with other items: you can have leather armor or a ring of protection, but only one applies.
* add feats, to taste.