Perhaps Congress should allocate itself the power to both grant pardons and/or to review&veto Presidential pardons.
I see it as a misdesign that the President has an exclusive, unchecked power to pardon, and without a corresponding power held by the people. In a Democracy, an unstated meta-rule is that a consensus of the people through its representatives in Congress, its consensus body, should always dominate decisions by the Executive.
The Executive is just one person, and subject to whim. As I see it, we grant them power not because we think it safer to put all that power in one place, but because we fear Congress might not achieve consensus fast enough or at all in some cases, and we might find ourselves crippled and unable to react fast enough for everything that comes up in the world. However, in any matter of disagreement between Congress and the Executive, if Congress does muster consensus, it seems to me that's generally preferable as a statement of what We The People should want.
A “review and veto” power would be useful as a check just in case there was ever a lawless President promising collaborating criminals a Get Out of Jail Free card. Whether or not one agrees that Congress should always win every contest of wills with the President, it's clear that the unchecked power to pardon fellow criminals must be reconsidered in at least some way.
As for issuing pardons directly, I'd not expect Congress to issue a lot of them itself because each would require a lot of politicians to agree about a single individual, and usually it would not seem worth the risk. But in the case of malicious prosecution by the DOJ, consensus of We The People should ‘trump’ executive power.
It might also have occasional value in other situations. For example, if Congress decides that marijuana possession, use, or even sale should not be criminalized after all, perhaps regretting that it ever was, then along with a change in the law, it could order blanket pardons of those convicted under prior law, rather than waiting for the Executive or the courts to sort that out, and assuring a more uniform application of new social understanding.
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The essay which became this post started as a tweet thread by me earlier today.
Our much-touted checks and balances have proven slow and ineffective at fending off attacks on the Constitution and our system of Democracy. We need to find ways to strengthen the power of the people against tyranny. That begins with discussions like these.