The kind of organization that McClellan was good at wasn't the kind that the Sec. of War needed to be doing.
George McClellan was good at organizing and forming an army, but he left a lot to be desired when given a field command. What if Lincoln had chosen to make McClellan his Secretary of War (a position he probably would have been much better suited to) than general-in-cheif? Who would have led the army, would the outcome of the war have been any different without Little Mac leading in the field?