The subservience of the Justice Department to the partisan politics of the Executive is a much bigger deal. The effects there are insidious, and often cannot be detected directly. This also allows the Executive to have a free hand, since most investigations are conducted by Justice.
At least with pardons and commuting, the President must do everything out in the open. That means that there is the potential for accountability. If only we had a parliamentary system, or a method of holding a recall vote.
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Cogito ergo spud -- I think, therefore I yam
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