The Executive having the power to pardon (or to refuse to prosecute) for crimes is meant as a check on legislative power to make life miserable through imposition of bad law. Just throwing that check away seems a bit destabilizing.
I mean, I'm with you on the the American justice system being capricious in terms of minor crimes being able to ruin a person's civil standing like marijuana possession has done; and rampant abuse of overclassifying certain types of crime as felonies, thereby disqualifying someone from participation in the civic process (something I genuinely have begun to abhor as I've gotten older, because of the perverse second-class citizen caste it creates with minimal if any remedy for restoration of rights without an absurd amount of pressure being applied by someone who has paid their debt to society).
However, it is putatively rule of law. Just rule of law with the assumption of input by men. Law is in itself a tool. A tool is nothing without the hand that wields it.
What angers me more is that we don't come down harder on those that maliciously attempt to use the tools of law against other tools of law. I.e. attempting to circumvent Constitutional rights through judicial review, or passing laws that everyone knows violate one Amendment or another and relying on the small number of Supreme Court justices and their auspices to just ignore passing a final decision on a case.
Frankly it seems like a somewhat intractable problem, but nevertheless, I can't deny that the United States at least puts up a good fight in terms of trying to make it work nevertheless.
Anyway, would love to hear your thoughts on it.
TL;DR Politics is downstream of culture.