Personally, I think Armors should only be as effective as their remaining percentage.
I.e.: If I have 50% armor left, an attack that deals 100 damage would deal 50 to armor, and 50 to health, regardless of if there's enough armor left to fully absorb the attack.
This should work similarly for status chances: if there's a 100% chance to get stunned, and I have 50% of my Magic Armor left, the chance I'm stunned should be 50%, not 0%.
Part of this is also in the attacks/abilities themselves though, for a system like that to work, there should both be abilities that have a lower chance to apply their effect, and ones that break above 100%(a 200% chance becomes 100% chance at 50% armor, ect.)
Also, about shields: they should at the very least get a Warfare tree ability that let's the user restore their armor(s), without dipping into Geomancer.