I suspect that the idea originally was to give some safety valve but if it is used more than a few times by a President, it makes a mockery of it and it should be removed as a power. How can a President ever decide that the entire legal process is flawed and their opinion is right? If the sentence was too long then change the sentencing guidelines.
Congress makes laws and impeaches presidents, courts judge constitutionality of laws and try cases of treason and presidents appoint judges and grant pardons.
You can't have impeachment without pardon, otherwise, there wouldn't be a check against judicial tyranny.