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.
On its own it is not that bad an idea for someone who carries a mandate of the majority of the population to be able to grant pardons.
Taken to the extreme, we could have an impartial legal system putting in prison criminals from an even mix of society, and then the president pardoning everyone from the majority group, leaving in prison only the minorities.
You want a majority to be able to decide who gets punished and who goes free, and even the best designed laws will have unforseen consequences. If the majority is 'evil', well there's just not all that much that can be done in a democracy. Yes it would be better to live in a dictatorship of the most virtuous person in existence, but if you ever figure out how to do that please let me know.