The key to understanding why President Obama picked deputy National Security Adviser Tom Donilon to replace Gen. James Jones has three grooves: one, Donilon is a civilian policy wonk loyal to the President who has been involved in every facet of foreign policy since the beginning of the administration; two, he's a politically-savvy Democrat; and three, he's an adviser whom the President can count on standing up to and pushing back against the military, when necessary.
The perception of Jones was that he was often indecisive, to the point where some of his colleagues would joke about the irony of his Secret Service code name: "Iron Hand."
But Jones, former commandant of the Marine Corps, was committed to the inter-agency process he oversaw and to the structure of the National Security Staff he helped create. This was deliberate on Jones's part: he believed the policy-making process was so "20th century" (in his words) and was committed to the new process he helped create, one that elevated issues like cybersecurity and climate change to the spectrum of issues that the National Security Staff wrestled with on a daily basis.
Obama selected Jones in part based on the private recommendation of Brent Scowcroft, the former Bush national security adviser, who told Obama that Jones would serve as an honest broker and would help the President navigate the complex terrain of civilian-military relations during a time of two wars. Jones had to first figure out how to handle the assortment of political and policy aides who knew the President better and could channel his voice; this led to friction that has lasted, in some degree, to this day.