I attended a workshop today regarding athletic shoes and orthotics. To my surprise there was a section on barefoot running. I was only Pedorthist (and only one that has tried barefooting and still is) out 100 podiatrists attending so don't shoot the messenger, I'm just repeating what I heard. The instructor talked about heel vs forefoot striking, cadence, Vo2 max, foot training/strengthening and shoe design. Everything in the discussion was based on scientific evidence and not anecdotal (he says).
He started off the talk about Abebe Bikila, the 1st Olympic barefoot runner. He went to say how great it was that was able to accomplish this feat. Then said "how many has there been since then?" "only 3 or 4" "If they thought they would win barefoot why are they all wearing shoes now?" "Athletes are only going to things to help them win" "will a forefoot runner beat a heel striker? NO!" He knows of no one that trains 100% barefoot, all use it as a supplement to shod running.
Some of the problems mentioned were decrease in Vo2 max due shorter strides, stress fractures, peroneal/posterior tendonitis. One thing he said that I thought was interesting is when someone transitions to BF they complain of plantar fascitis. He said 9/10 it is not, the have strained the intrinsic plantar muscles that are above the fascia. Another positive thing was that people that have patellofemoral pain improve when the get out shoes, forefoot running puts less stress on the knees. Also talked about strengthening and proper transitioning.
He picked apart minimalist shoes, lack of torsional stabilty, no cushioning, too flexible, no toe spring, no heel rise. VFF, Saucony and Nike were the only shoes he brought in. All in all the Dr. were not impressed with the barefoot "fad".
I'm a runner who began wearing VFFs last spring, and wore them throughout the summer as my everyday walking shoes - I never transitioned to running in them. I have had re-occurring pain in my right foot since then and recently switched back to walking shoes with arch supports.
I went to a podiatrist when the discomfort persisted (though the pain had improved immensely with arch supports). She diagnosed me with posterior tibial tendinitis and recommended custom orthotics to keep my feet in the correct position. When I asked her about minimalist footwear, she felt strongly that they are a bad idea, similar to the other podiatrists at the workshop you went to.
While I'm sure barefoot walking/running works fine for some people, it did not for me and I now refuse to wear barefoot shoes. Part of the problem may be that I have pretty high arches that need support, I don't know. I think minimalist footwear requires more research to determine who would benefit most from transitioning to this type of footwear.