while im not particularly good at balance, i will just throw out a Magic Item solution i made, as well as leave this link to my feats thread where i did a small bit of rebalancing to feats and came up with a few others.
anyway, Undead should be a Construct subtype, and Construct (the entire type) should not grant critical immunity against bludgeon weapons unless incorporal.
Armor and Shield: Keep, even though you want to kick shield, it is different from deflection. Rebalance armor and shields
Size: Keep it, but axe Size attack bonuses
Competence, Circumstance, and Dodge: Roll together. These are litterally the same thing for AC purposes
Deflection: Eliminate as an Armor bonus, instead make a % chance for blows/projectiles to go wild.
Resistance: Roll into Protection (which incedentally, you missed)
Sacred/Profane: No, keep em separate, and also make it so they cancel eachother out, and also corrispond to alignment specific bonuses or penalties. Figuring out a name for a L/C axis would be nice too