I think it has more to do with the way our characters are modeled. The slight "heel" we have when barefoot allows all shoe models to fit similarly. Without that, they would have to adjust all character heights and possibly even running/walking animations to accommodate the lack of a heel. I've finished the story and I can't remember any instances with a barefoot model, aside from cutscenes that don't depict anyone walking without shoes, but please remind me if I'm wrong. I like the idea, I just don't know how easy it is to accomplish. ^^