> Congress already decides how much to spend and on what weapons systems for the various branches of the military.

Congress directs some times and defers other times. Congress absolutely does not direct every pentagon spending program.

> The authority to command the armed forces is directly under the executive

The EPA is an "executive department" as described by article two of the constitution the same as the department of defense. If the founders expected congress alone to execute executive authority (except in the special case of the military) then the constitution would have been written that way and the EPA would have been created as a body that reports to congress. Congress was obeying the constitution when they created the EPA under the president, just as they were when they created every other executive department.

My argument is that we have been lax with the separation of powers. Congress is required to declare war before the President can direct the armed forces into combat, for example. This has failed recently. Congress also must not declare a permanent generic war, and then leave it up the the executive branch free to do whatever it wants with the military. Or, if they declare war on French Guiana, that doesn’t give the president freedom to attack Georgia.

The argument is not that the EPA should report to Congress instead of the President. The argument is that the EPA should be limited to doing what the laws Congress passed actually says. It is the executive branch’s responsibility to implement the law, not create, implement, and judge cases like they have been doing.