Ultimately, Clinton would be a stronger candidate against McCain in the general election.
My preference is a general election between McCain and Obama, as McCain has a higher chance of defeating Obama than he does of defeating Clinton.
Obama's inexperience and past statements would come back to haunt him in the election, and who knows what other shoes could drop about Obama during the course of the campaign.
However, McCain confusing Iran with al Qaida will definitely hurt him when he's trying to sell himself as a foreign policy wonk.
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