The Pentagon's allies in Congress fought long and hard against losing control and in the end gained assurances that the chain of command would not be
broken and the military would not find itself losing out.
So exactly how much control will the new director really have?
The devil will be in the detail: exactly how will authority will be divided in practice between the new director and the Pentagon?
Can the new official really set tasking across all the different agencies, or will he instead become an impotent figure, setting priorities but
without the budgetary clout to force people to carry them out?
Others also ask whether it is dangerous to create a director figure who does not have his own institution like the CIA behind him.
Could he end up a floating manager without real institutional clout who is too distant from the people in the field doing their job?
21st century intelligence
The next question is how much energy the process of re-organising consumes. One parallel may be with the Department of Homeland Security, where
multiple agencies were pulled together but have taken a long time to adapt and learn to work together.
Some fear that a similar upheaval might distract the intelligence community from its day-to-day work.
And the last major question is how much difference, broad institutional re-organisation will really mean to people on the ground.
The inquiries into problems over Iraq's weapons of mass destruction made clear that the failure was not one of the wrong structure but one of not
having enough spies on the ground and not analysing the intelligence in a sufficiently balanced way.
These are problems that Porter Goss, the new chief of the CIA, is trying to address, but which are quite independent of the reforms that Congress has
Before this week America's intelligence structure had barely changed since the start of the Cold War.
Reformers hope that the new structure will be one capable of dealing with the very different trans-national threats of the 21st century.
But it may take some time before it is clear just how much difference reform has really made...