First, for the record, I like barefoot running, I own a pair of Vibrams (for three years), my favorite book of two years ago was Born to Run and I buy some of the caveman ideas (like doing my best to eat paleo).
When I was dealing with achillies problems heading into our Olympic training year as a push athlete I had severe achillies tendonosis on my left side. We did everything to try to get it better, soft tissue, ultrasound, taping, foot strengthening drills. Finally I just decided to do a few barefoot runs. Not sure why. I guess it's an example of listening to that inner voice. It hurt at first and then just got better. I did 8x60 meters. Each one a bit faster then the previous. It worked......for me. Sample size of N=1.
OK. Now lets dive into the negatives. First the caveman idea. I'm going to go out on a limb and say, no cavemen or cavewomen were overweight. I think they were lean and mean and always moving. No one had a spare tire or as my friend calls it "middle heavy."
I doubt if any of them did things repeatedly for aesthetics. Hitting bench press every Monday. So what I'm saying is, I'm betting there were not a lot of muscle imbalances. Also, food for thought, no one ran on concrete or asphalt.
I see to many people with weak hips, if your hips are weak, you will lose your arch in the foot. Loss of arch means more pronation. Pushing off a pronated foot is a calf problem waiting to happen. Can you stand barefoot on one foot for 30 seconds without falling? Can you do a clean lunge? First strengthen your hips.
I've heard the arguments. So and so does it. One of the most powerful, dangerous and easy things, is the comparison with someone that is doing it. Recently in Runners magazine a guy ran a marathon in like 2:27 barefoot. Or the Kenyans run barefoot growing up. (ever notice they don't run barefoot anymore). Look if they are running that fast, they are a gifted runner. They were put together biomechanically efficient. Compare yourself to you.
The first big barefoot boom was the Nike Free's that Nike put out after talking to the Stanford Cross Country coach. They noticed he had his athletes run 100 meter repeats barefoot in the pristine grass after some workouts to strengthen there feet. Nike saw dollar signs. Pay attention. These were elite college cross country runners. They had a gift and were only running 100 meter repeats a few times a week. Not there running workouts.
Does everyone need an orthotic, absolutely not. But if a factory guy has sore feet every day and works 10-12 hours per day. They may be a lifesaver for him.
Like all things fitness, the pendulum usually swings in one direction to hard such as the 150 dollar running shoe with posts/arch support/extra cushioning and then swings equally far in the other direction. Running in nothing. The answer usually lies in the middle.