I'm concerned about the possibility of long-entrenched partisans in the Executive Branch undermining our next President the way many of them did to Kennedy. Here's a few names:
Allen Dulles: The first civilian director of the CIA and one of the brain-powers behind the Bay of Pigs invasion.
Curtis "Bombs Away" LeMay: Air Force Chief of Staff under Kennedy. Kennedy believed he could assuage his right-wing critics by appointing LeMay, but he only emboldened them. During the Cuban Missile Crisis, LeMay wanted to bomb the missile sites. While he admitted that he could only guarantee that he would get 90% of the missile sites (a guarantee which later turned out to be rather generous), he also opined that the Soviets would probably not retaliate. Kennedy found that remarkably naive, especially coming from a four star general, and did not follow his advice. Personally, I don't think LeMay was naive, just disingenuous. It's not that he didn't think the Soviets would retaliate; he just didn't care. "Bombs away". Afterwards, he said, "We had a chance to throw the Communists out of Cuba. But the administration was scared to death (the Soviet Union) might shoot a missile at us." Yeah, what's one or two nuclear missiles in one or two U.S. cities, right? If the LeMays of the world had had their way, we'd be living (or not) in a post-apocalyptic nightmare. We avoided a nuclear exchange by the skin of our teeth as it was. I guarantee there are many more LeMays waiting in the ranks under this administration. Clinton or Obama will have to root them out and help them find their way into retirement.
Richard Helms: The man behind the curtain at the CIA while John McCone was director. Directed many assassination attempts against Fidel Castro and other foreign leaders, often at the expense of diplomatic efforts on the part of the President.
There are others, but these three are sufficient to demonstrate that the President does not, by himself, run the executive branch. If the next President does not clean house within the first 100 days, he or she will likely be stuck with whatever trolls this administration has left hiding under the bridge.
Both Clinton and Obama have retired four star generals in their corner: Clinton has former NATO Commander Wesley Clark in her corner and Obama has former USCENTCOM commander Anthony Zinni in his. I would suggest that both these men be put to use in the next administration: Zinni as SECDEF and Clark as CIA director. Or vice versa. Hayden has to go, and his trolls will be waiting to undermine Clinton or Obama. It is absolutely vital that we have a strong CIA director to root them out, and either Zinni or Clark would fit that bill.
On edit: I forgot about DHS. This department, created under Bush, will be filled entirely with Bush partisans. One way to tame the CIA beast would be to incorporate it under DHS rather than allowing it to continue as its own nebulous independent agency. In that case, I would favor Clark or Zinni as DHS secretary rather than CIA director. Right now, DHS is still finding its identity, and while it will be stocked with Bush partisans, it hasn't been around long enough for any of them to be "entrenched". Big opportunity to change the face of DHS and the CIA.
I'm actually split on this one with regards to Sen. Obama and Sen. Clinton. I think Sen. Clinton would be better suited to this task, but I think Sen. Obama would be more likely to actually carry it out. I lean toward Sen. Obama if he gets the right people behind him (e.g., Clark and Zinni), but this is one area where he can't try to "reach out". These people will take any attempted outreach as a sign of weakness, and they will absolutely try to exploit it. I hope he's wise to this fact. If he has Zinni as an advisor, I'm sure he is.
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