I think it's part of a psychological aspect of story-telling. We, as humans, know exactly what we're capable of, so in order to make Superheroes and Villains super, they have to be something beyond human. Even Batman and heroes like him fall into the category, he is super because he defies what we would normally expect a human to be capable of, in mind, body and spirit.
It's possible that Humans in this stage of their lives are capable of a lot more than certain alien races or species, and being the dominant species on a planet that is the center of the multiverse couldn't be without some kind of perks. I guess, for the moment, Humanity's shared power is that we simply refuse to die.
It can also be said that 'Super' is usually down to perception, and one of my favourite supervillains, Syndrome, utilises this aspect brilliantly:
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