The Bush administration is enamored with the concept of broad executive powers. More than any social issue like abortion, it is this issue that drove their choice of nominees for the Supreme Court.
In 2001, John Yoo's memo justifying torture basically stated that the president had the right to break any law in the name of national security and could not be held liable for any actions taken as Commander in Chief. No-one stopped to mention that the stability and longevity of our democracy rests on the checks and balances that come from three equal branches of government. No, instead, this administration might take as it's motto "some branches are more equal than others".
Specifically, the Yoo memo states that "the President enjoys complete discretion in the exercise of his Commander in Chief authority" (emphasis mine). A full fourth of the memo defends this position, explaining that neither Congress nor the courts can tell the President what he can and can't do as Commander in Chief. No laws can restrain him in that constitutional role. And even if an argument can be made that the law applies, the memo offered two fully developed defenses.
Of course, this is the same memo that the administration retracted just before the Gonzales hearings, with a quiet footnote that the retraction didn't apply to the analysis on Commander in Chief authority. So that analysis stands. And Bush doesn't want it challenged in court (hence the efforts to move the Padilla prosecution to criminal court). He needs friends on the Supreme Court, friends that will agree with Yoo's views on presidential supremacy. He needs friends to codify his "some branches are more equal than others" view of our government. We can't let him have them.