I fancy myself a pretty bright guy. And yet, put me in at governor of Illinois or CEO of GE or as the captain of a navy ship, and I will make a godawful hash of it, because intelligence isn't enough to do those jobs--you also need to have the experience of running parts of them, or of running comparable operations, and detailed knowledge of how these very complicated organizations work.
President must be far worse. Everyone who ever talks to you not only has an agenda, they're out on the right end of the intelligence and manipulativeness and people-skills distributions, and you are their main focus. Most of us have been tricked by dishonest people, or felt the unpleasant push of a skilled salesman trying to get us to buy something. Imagine that all the time, except they're world class salesmen, and all your information about what they're selling and what a reasonable price would be is controlled by equally manipulative salesmen.
Think about a conflict between Obama and Geithner. Obama has few contacts in the financial world, and those are mostly people he's gotten to know only since he was running for office. Geithner has been plugged into that world for his whole professional life. Obama has the authority to fire Geithner, but in many ways, he's much the weaker of the two.
And that applies everywhere--Obama might have wanted to close down Guantanamo and investigate the guys who ran our illegal domestic spying and torture programs. But when his advisors tell him that doing so will destroy the NSA and CIA, who does he ask for confirmation. He doesn't have a dozen old friends he's worked with for years on these issues, guys he knows well enough that it would be hard for them to lie or spin him much. He probably had some people like that in Illinois politics, but he had no time to find them in Washington--when he arrived, he was already effectively running for president.