On the ninety-ninth episode of the Molsan Method podcast, I answer the itemization question about choosing one piece of gear over another in World of Warcraft. (10:03)
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On characters that still are subject to the GearScore hassle, I like to do what you suggest, i.e. equip the higher gear score item.
However, if I have items with a lower GearScore, but higher benefit for me (e.g. plate boots with haste on them instead of armor penetration for a retri pally), I will keep those items in my inventory and equip them right before going into combat. No one looks at your GearScore during combat, and you’ll have a higher DPS output than with the stupid “better GearScore” crap.