As a warrior, I treated armour and defense separately. Agility raises both offense and defense, but I was mainly concerned with the offense. For armour, I went with the highest armour class first, then whatever bonuses I could get. Better bonuses might convince me to choose a slightly lower armour class, but I never looked specifically for defense boosts.
Even for an archer or mage, the chance of getting hit and how much damage taken when you are hit are separate (though similar) concepts. It depends on your playing style for which would be 'better'. The only time you even have to make a choice between them is when you have two pieces of armour, one with a (better) defense bonus but a lower armour class.
