I think the key to making sense out of this is to remember that each defence works against a completely different kind of attack.
Some attacks such as virtually all of the fighter, ranger and paladin attacks are made against AC. This implies that while dexterity and intelligence are important for allowing lightly armored characters to dodge the attacks, the attacks themselves are inherently difficult to dodge.
While the spell casters, orbs, blasts, bursts, etc... are typically against REF. A quick "twitch" might be all it takes to avoid a magic missile, because they are relatively easy to dodge and if you are hit, these attacks agnore your armor.
Think about it, I suspect we can all agree that its probably easier to dodge a dodgeball from 30' away (heck Iv'e even seen them dodged at 1'), than it is to dodge the swing of a sword from an opponent standing 3' in front of you.
Your AC represents your total ability to avoid/block/absorb most typical melee and ranged attacks.
Your Ref represents your ability to dodge attacks that are typically ranged, and certain characters may excel at dodging these types of attacks.