This is the first I've heard of The Skeptoid so I can't address his writings, but he does have an interesting post about barefoot running. And he approaches the subject with skepticism which is a good thing.
That evolution has made us into bipeds that walk and run barefoot across the savannah is not a perfect argument that we're well adapted to do so. There are many examples in nature of creatures who evolved detrimental traits. The giraffe's laryngeal nerve runs all the way down its neck into its chest, loops around its aorta, then runs all the way back up to its larynx; making it absurdly long and prone to many types of failure. The Irish elk developed antlers so large that the energy required to grow them exceeded the available food sources and the species became extinct. The mating ritual of the Kakapo flightless parrot is more likely to attract a predator than a mate. The retinas in all vertebrate eyeballs are inside-out, creating an unnecessary blind spot. The list goes on forever. The point is that evolution does not create perfectly adapted creatures; it creates adequate creatures.
Funny he should mention the laryngeal nerve in giraffes. The bizarre path taken by the laryngeal nerve is true for all mammals, including humans. It's just more pronounced and noticeable for giraffes since their necks are so long. I have no idea what failures of the nerve he's referring to. I've never read anything about that nor can I find anything on the subject. But he does make one good point, that being evolution does not create perfectly adapted creatures.
But enough about evolution. The article is about barefoot running. The lack of hard data means we really don't know if it's better or not for you. But I can say that it works for me.