I have previously argued that, while the central problem of international relations in the 20th century was states that were too strong (Germany, Imperial Japan, the Soviet Union), the primary problems of international relations in the 21st century are states that are too weak (Afghanistan, Pakistan, Mexico). Thomas Friedman agrees in the linked New York Times column, which has vast implications not just for the State Department, but also for the Department of Defense.
Super (Sub) Secretaries - Thomas Friedman, New York Times
It is way too soon to say what policy breakthroughs Secretary of State Hillary Clinton will be known for at the State Department. But she has already left her mark bureaucratically. She has invented new diplomatic positions that say a great deal about the state of foreign policy in these messy times. I would call them "The Super Sub-Secretaries of State."
Mrs. Clinton has appointed three Super Sub-Secretaries - George Mitchell to handle Arab-Israel negotiations, Richard Holbrooke to manage Afghanistan-Pakistan affairs and Dennis Ross to coordinate Iran policy. The Obama team seems to have concluded that these three problems are so intractable that they require almost full-time secretary of state-quality attention. So you need officials who have more weight and more time - more weight than the normal assistant secretary of state so they will be taken seriously in their respective regions and will have a chance to move the bureaucracy, and more time to work on each of these discrete, Gordian problems than a secretary of state can devote in a week...
More at The New York Times.