Neurological Perspective
With shoes we block the communication highway from the outside world to the feet and body. Think of your body as one big satellite dish picking up information through tiny sensory receptors through out your body. There are literally thousands of these specialized receptors in your feet, designed to send messages to the brain via the central nervous system and interpreted by the brain and spinal cord sending back an appropriate command through our motor response - all so we can react and move in a quality fashion. Shoes block the information from coming in, diminishing the quality of the movement which sets us up for injury.
Think about wearing gloves all day to protect your hands. Would you be able to perform your tasks as well? This is how shoes have become a burden and causing many compensatory problems that are classified under "overuse" injuries.