The reason Woolsey got the job was because he was considered someone who could be controlled. It wasn't about who was best for the job, it was about politics. Very simply, the international community and the U.S. government had been sparring over control/access for quite some time. The idea of a U.S. military officer in charge of Atlantis therefore concerned them. It was one thing to make such a concession when they were afraid of an Asuran attack, but as soon as they weren't shaking in their boots over a possible imminent attack, they reverted to their standard mode of operation and decided to make a power play for increased influence over the Atlantis expedition.
Could they have selected the most qualified civilian candidate for the position? Sure, but they already did that with Weir and she stood up against them and their agenda. Hence, the best option, for their intentions, seemed like the weaselly, by the book pencil pusher type. Thus, Woosley got the job. So all the reasons that people cite over why they don't think he should have been the leader are exactly why he was put in charge. Of course, he did end up standing up to them so that didn't work out so well, but that's a different matter.
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