An idea I saw floating around some discution threads on the American Civil War a while back was to split the political and military sides of the Confederacy to be almost totally seperate entities.
In OTL Davis was the commander of all confederate forces and he ran things according to whom his favorites were and by his ideas of offensive-defence.
One of his major quarrels with P.G.T. Beauregard and Joe Johnston was that those two general's wanted the overall strategy planning to be in the hands of experianced generals like themselves and not left to the politicians while Davis wanted to manage the whole war his way without the interferance of the generals.
As a result Beauregard was assigned to a backwater, out of the way corner of the war while Joe Johnston only got a proper chance to prove himself twice, once in the Peninsular which was cut short due to his injury and the other time in the Atlanta campaign when Davis relieved him and replace him with Hood when, by all right, Beauregard should have gotten that job.
So the idea then is to create an office when the Confederate states are formed establishing one overall Supreme Commander of all the Confederate military giving them the power to over-rule the president in military matters.
Which General would get the job and how would such a post change the course of the war?