It's just hard to beat several million years of evolutionary adaptation, even accounting for the fine craftsmanship of Church's handmade English shoes (all the rage in France, when I lived there).
Nonetheless, just as I blogged in my entry Learning to Walk a few months back, barefoot or nearly so is best. I love my Vibram Five Fingers (which have been dubbed my "feet" by my wife; as in: "should I toss down your feet?") and I even walk just plain barefoot now and then. People tease me about the soles of my feet, often on display, and thoroughly black.
It's quite easy to get used to.
Matt Metzgar dug up a study, and guess what? Shoes increase stress on your knees and hips (pdf). He quotes a portion and I can personally attest to part of the speculation: "A final explanation of the biomechanical advantages of barefoot walking may be attributed to increased proprioceptive input from skin contact with the ground compared with an insulated foot contacting the ground." This is exactly what I have been noting when discussing the issue with people (the Vibrams are quite a conversation piece). Just as I have often commented that flexible, intermittent fasting gives you high resolution into your personal hunger and appetite signaling, so too does going barefoot outside where there exists all manner of things that can cause pain and injury give you high resolution into your walking. After a time, you don't even notice small sharp pebbles as you lighten your step on the fly, instantly. You also gain awareness of your peripheral vision and avoid stepping on things you shouldn't — without even being conscious of it. At first, it's sensory overload. After a time, it becomes thoroughly natural. Go figure.
Now, I don't know about you, but my gut reaction is that any modern thing that actually cuts me off from sensory perception (the root of knowledge of reality) had better be good and damn necessary. Guilty, until proven innocent, I'd say. Given the added stress on joins and hips, and the resultant chronic injury with surgery and replacement experienced by so many, I'd say the jury is in. …So go frollic barefoot. What the hell? You know people are going to envy you for it.
Walking. Bi-ped hominoid. It's pretty damn fundamental.