Matt Yglesias lays out the problem with keeping Gates on as Secretary of Defense:
The problem with retaining Robert Gates as Secretary of Defense is the same as the problem with the idea of appointing Chuck Hagel or when Bill Clinton about William Cohen -- these guys are Republicans. It's desperately important for the Democratic Party's leaders to avoid re-enforcing the idea that Democrats can't run national security. If you find a moderate Republican with sound views on key environmental issues and make him or her head of the EPA, that says "climate change is an important issue and there's bipartisan support for taking action." If you put a Republican in charge of the Pentagon it says "Obama likes diplomacy, but even he knows that when the going gets tough you need to call in the GOP."
Good point. I still don't think it's a terrible idea to keep the guy around for two years if you're planning on withdrawing from Iraq during that time--that would ideally leave Obama with six more years to burnish the party's national security credentials. But I concede that you get the most bang for your buck, message-sending-wise, at the outset of your administration. So there would be a significant opportunity cost in terms of re-branding.