Through Bush, Clinton and Bush, the National Security apparatus grew in influence and power. With the Obama administration, it was reported that the National Security Adviser would be given the position of influence within the administration akin to that held by Henry Kissinger in the Nixon administration, as Obama was selecting General James L. Jones to be National Security Adviser, and "is considering expanding the scope of the job to give the adviser the kind of authority once wielded by powerful figures such as Henry A. Kissinger."http://www.washingtonpost.com/wp-dyn/content/article/2008/11/21/AR2008112103981.html
This would be a change from the Bush jr. years, where the National Security Adviser lost out in influence to the Pentagon (under Rumsfeld) and Vice President Cheney, until 2006, when Rumsfeld was replaced with Robert Gates as Secretary of Defense, who aligned himself with Rice as Secretary of State to roll back the influence of Cheney. Gates was kept on as Secretary of Defense in the Obama administration.http://www.washingtonpost.com/wp-dyn/content/article/2008/11/18/AR2008111803422.html
Henry Kissinger wrote an op-ed in the Washington Post where he praised Obama's National Security team, and in particular, General James Jones.http://www.washingtonpost.com/wp-dyn/content/article/2008/12/04/AR2008120402863.html
General James Jones, within weeks of the Obama administration taking power, spoke at a Security Conference in Munich, and said, "As the most recent National Security Advisor of the United States, I take my daily orders from Dr. Kissinger
, filtered down through Generaal Brent Scowcroft and Sandy Berger, who is also here. We have a chain of command in the National Security Council that exists today.
Obama even merged the Homeland Security Council into the National Security Council, giving it an incredibly powerful influence over not only foreign, but domestic policy.http://www.washingtonpost.com/wp-dyn/content/article/2009/05/26/AR2009052603148.html
The National Security Council (NSC) under Obama is "a very powerful NSC" and General "Jones declared that Obama's NSC would be "dramatically different" from its predecessors, in terms of enhanced power and government-wide coordinating authority across a larger group of federal agencies involved in the modern national security project."http://thecable.foreignpolicy.com/posts/2009/02/10/james_l_jones_and_the_committee_to_run_the_worldhttp://www.washingtonpost.com/wp-dyn/content/article/2009/02/07/AR2009020702076.html?hpid=topnews
According to the State Department's Special Envoy to Afghanistan and Pakistan, Richard Holbrooke, General Jones "has served as an important filter between the president and the military," especially in regards to Afghan policy.http://www.nytimes.com/2009/05/07/us/07jones.html
General Stanley McChrystal, on the other hand, while FAR from being "one of us" (as one forum posted postulated), is rather of a different breed of foreign policy thinkers, and is a hold-over from the Bush years. During the Bush administration, McChrystal ran the Joint Special Operations Command (JSOC), which "is the military's most secretive branch
(many of its components are still not officially acknowledged to exist), charged with its most secretive missions
— identifying, tracking, killing, or capturing and interrogating the highest-level members of Al Qaeda and other terrorist groups. That it does so in conjunction with the CIA, DIA, FBI, and other intelligence agencies only makes JSOC's task more sensitive."
Read more: http://www.esquire.com/the-side/feature/who-is-stanley-mcchrystal-051909#ixzz0rkxv2W97
Pulitzer Prize winning investigative journalist Seymour Hersh gave a speech in which he revealed that, "former US vice-president Dick Cheney headed a secret assassination wing that targeted America's enemies abroad
." That unit was JSOC, then under the command of General Stanley McChrystal. This "assassination squad" was "not just in Iraq and Afghanistan, it's in a lot of other countries, in the Middle East and in South Asia and North Africa and even central America." http://gulfnews.com/news/region/palestinian-territories/you-can-t-authorise-murder-hersh-1.68504
Near the end of the first year of the Obama administration, the Special Operations Chiefs in the Pentagon were gaining increased influence with Obama on foreign policy, and they were intricately connected with General Stanley McChrystal. http://washingtonindependent.com/67136/special-operations-chiefs-quietly-sway-afghanistan-policy
Jones himself, is closely allied in foreign policy with Secretary of State Hilary Clinton and Defense Secretary Robert Gates.http://www.washingtonpost.com/wp-dyn/content/article/2009/02/07/AR2009020702076_2.html?hpid=topnews
What likely took place, was a rift between the National Security Council as the principle source for foreign policy decision making, and other "back channels" that were so prominent in the Bush administration, such as those between Cheney and McChrystal. As McChrystal was gaining influence, he became arrogant and took the internal divisions within the White House and exposed them to the public. For this, McChrystal is being hung out to dry.
So, like in all administrations, there are great divisions and power struggles for who will control foreign policy. It seems that in the Obama administration, that position is taken by the National Security Council.