It is textbook civics to assert that the three branches of the U.S. federal government are separate but equal. While there should be checks and balances, most of the activity of government should be done through the legislature, as the most broadly representative of those branches. We are far from this ideal and moving in the wrong direction.
Just look at where the manpower is in the federal government--civil servants working in cabinet departments headed by political appointees of the President. Consider today's news story in which the Office of the Vice President is accused of deleting sections of the Congressional testimony of the head of the CDC on climate change:
Vice President Dick Cheney's office was involved in removing statements on health risks posed by global warming from a draft of a health official’s Senate testimony last year, a former senior government environmental official said on Tuesday.
The former official, Jason K. Burnett, made the assertion and described similar incidents in a three-page letter to Senator Barbara Boxer, a California Democrat who is the chairwoman of the Senate Environment and Public Works Committee. He then stood with her at a news conference at which she excoriated the Bush administration.
Congress has allocated the money to pay for expertise in the CDC and other agencies. Why should that expertise be filtered through any other part of the executive branch before it gets to Congress? Why should all of that manpower not be directly accountable to Congress as opposed to the President? The design of the system lends itself to this sort of interference.