Alluded to earlier in the thread, but one thing that bugs me is Armour Class, as a concept.
I grew up playing Warhammer, and only came to D&D as an adult. It took me a while to acclimatise to the nonsensical abstraction of AC. The Warhammer approach (copied over into WFRP) makes much more intuitive sense. Amour affects how much damage a hit does (as, for that matter, does strength), not whether the hit is likely to hit. I get that it's all a gamey abstraction; but D&D already has a 'roll to hit/roll to wound' distinction. Which makes it even weirder to me that they moved part of what, conceptually, belongs to the damage roll into the 'to hit' roll.