The idea of having someone be both ambassador to Germany and the EU seemed liked a bad idea as the two are not one and the same and appointing the same person there just plays into the idea the EU is German dominated.  While the two are closely connected, but to have separate ambassadors who would off course work well together.  Also Stephane Dion is one of the first ambassadors we've had to Germany who doesn't speak German (although not a requirement it helps).