I do like the potency / propriety rune system, and it is not such a problem in itself because it allows you to customize your weapons and armor as you see fit through the adventure.
For example if you have an heirloom weapon that is very dear to your character, you can just extract the potency rune from the amazing +3 greatsword you found and apply it to your beloved weapon.
The stat boost items are the only problem imo. These items are a real pain because you have to get them somehow. If you don't or your GM doesn't drop you one, you are screwed until the end of the adventure.
The solution I propose is to completely remove these overpowered items and transform their effect into a sort of "rune" that you can apply to any magic item. That way you can now keep the dancing scarf that you found and wanted to sell in order to buy your belt of strength, and you can even improve it to make it really unique and very important to your character.