It appears clear to me that Ryan Crocker will be an upgrade over Karl Eikenberry as ambassador to Afghanistan.
As to the other moves, in my mind, Secretary Gates is the finest Secretary of Defense in our history. Mr. Panetta, although talented, probably won't come close to Secretary Gates. Secretary Gates has been fighting the DoD bureaucracy since the beginning of his tenure asking for budget cuts and to spend money on "stuff" we need now, not 20 years from now; he was a visionary. Mr. Panetta, a Washington insider, is not a visionary.
With regards to the GEN Petraeus move, it seems like a lateral move that just allows him to collect his Army retirement check and a paycheck for being CIA Director, while keeping him in the United States with his family (most of the time). This move also keeps him off the ballot, an added benefit to career politicians that view him as a potential threat.
Finally, Lt. Gen. Allen will do a fine job in Afghanistan if his work in Iraq's MNF-W is any indicator.
Here is an excerpt from the article:
Perhaps the greatest risk of the reshuffle comes in Afghanistan, where the departure of Gen. Petraeus will remove America’s most skilled military commander from a campaign that appears to be teetering between success and failure. Lt. Gen. Allen, however, was a key contributor to the successful turnaround of the war in Iraq; and Mr. Crocker offers a major improvement over his predecessor, Karl Eikenberry, who contributed substantially to the souring of U.S. relations with Afghan President Hamid Karzai.