I have yet to see one good historical example or even a hypothetical argument given for presidential pardon to exist.
Also, if there really is a separation of power than President should not meddle in Judicial branch affairs.
Its an imperfect system, just following the script that law provides will lead to injustices. Having an escape hatch is a good thing, even if it is occasionally abused. I would support federal/state congresses overturning pardons though.