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.
Regimes have toppled in response to popular uprising against imprisonments perceived as unjust. Having a system of governance without a way to rectify that seems unwise to me.
The check on Presidential authority, in turn, is impeachment. It's not a perfect system by any means, but in my estimation it's a good one.