Most Servants would lose to Herakles, but the fact of the matter is a so-called "underpowered" Servant with practically no one aware of his legend wrecked almost half of the lives he had in stock. It was to the point where even Herakles wanted a proper rematch against EMIYA, because he was that impressed with his skill.
As a warrior, EMIYA is plenty powerful and dangerous. As a person, though, he leaves a bit to be desired.