alt Hacker Newswhy is that crazy? legislative supremacy is an extremely common pillar of many theories of democracy. the executive has only the powers enumerated in the Constitution and explicitly granted by Congress. if Congress wants to set up an agency independent of POTUS, that "should" (scare quotes because who knows what this activist SCOTUS will do) be well within its constitutional purview
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The legislature also has only the powers enumerated in the Constitution. As "create independent agencies" is not one of those powers, it comes down to a matter of interpretation as to whether one of the powers granted to Congress implies the ability to create independent agencies. But once you enter the land of interpretation, it's, well... open to interpretation, and thus it's not unreasonable for someone to take issue with a certain interpretation.
The Constitution was, after all, written by people who had just fought a war to throw off an overreaching executive. No goal was more important to them than to prevent another one.