I say the Unitary Executive is a valid option of constitutional interpretation because it is directly gleaned from Article II of the Constitution. To quote directly from the Wikipedia article:
The theory relies on the Vesting Clause of Article II which states "The executive Power shall be vested in a President of the United States of America." Proponents of the unitary executive theory use this language along with the Take Care Clause ("The President shall take care that the laws be faithfully executed...") to argue that the Constitution creates a "hierarchical, unified executive department under the direct control of the President."
While this might be a valid interpretation of the words of our Constitution, our tradition has evolved away from a strict implementation of the unitary executive theory. While the president retains vast power to direct the executive ship, there are areas of day-to-day governmental operation that we seek to rest above or beyond the realm of politics. For example, the Federal Reserve is not directly answerable to the President, although it is technically part of the Executive Branch. Same goes for independent agencies such as NASA or the Federal Election Commission. These agencies work in areas that Americans generally agree should remain free of the influence of presidential priorities and partisan wrangling. For the FDA, science is science no matter who is president.
Nevertheless, John Yoo thinks that everyone in the executive branch should be in lock-step with the President: "Every subordinate should agree with [the president's] views so there is a unified approach to the law..." He goes on to elaborate why the unitary executive is necessary:
“The president reacts to unforeseen events and emergencies that Congress can’t anticipate … like Sept. 11, that are outside the anticipation of written laws,” said Yoo. “The framers wanted a presidency that’s unified and can operate with speed and secrecy so they left [the office] with ambiguous limits on its power. It was not carefully defined, deliberately.”
Regardless of the defensibility of the Unitary Executive, Yoo's claims springboard into waters way beyond the realm of the theory. While Alexander Hamilton writes repeatedly in The Federalist Papers that the country needs an "energetic executive" or an "energetic government," I am not aware of any reference from the Founders that the Government should operate in secret. And they most certainly were not ambiguous on the limits of the presidency's powers. Checks and balances along with separation of powers are central to the framework that the Constitution erects. The president's realm is to execute the law, not make it or reinterpret it or ignore it. And the president (nor the Administration) certainly may not break the law, a la FISA-style.