I was reading through an older study(pdf) that looked at the low percentage of foot problems in unshod children. I also noticed where they discussed the different effects of footwear:
I saw where Terra Plana has come out with a new type of barefoot sandal – "Achilles".
I should mention that sandals do alter the foot mechanics as compared to barefoot. At least this was true for the sandals in the study, which had fastenings in the front and in the back. Maybe sandals with only front fastenings will activate more foot muscles.