1. Evolution rarely optimizes for only one function, i.e. running economy.
Also, humans have only run on hard surfaces for a short period of time.
Despite the thoughts of some posters on LRC, few people select mates based on running efficiency.
2. Many studies have compared barefoot running vs. shoes and typically there is no significant difference.
The weight costs energy but the shoe cushioning saves energy because the muscles don't have to do as much cushioning.
The two counterbalance each other.
But, if a shoe is light and cushioned (e.g. Vaporfly 4%), then on hard surfaces, the shoes saves energy vs. barefoot.
3. It would be interesting to measure the energy cost of running on natural terrain while barefoot vs. with shoes in runners who are experienced with both. We have found that if weight is factored out, too much cushioning can negatively affect running economy. But the responses are individual and that was with EVA, pre-PEBAX (the foam in VF4).