“Reappointing Bernanke, who is from an opposing party, is a signal that such meddling won’t be applied to the Fed and that the Fed will be allowed to regain some of its autonomy vis-a-vis Treasury. Not reappointing Bernanke would make the markets very nervous about the future autonomy of the Fed.”
I think this might be the most important factor and it will be interesting to see which way Obama goes.