I'm in the middle of reading Jefferson Davis' account of the American Civil War, so naturally the issue of how the CSA could have done things differently and/ or better comes up.
As always with these, I think once the war started and the federal government and the North were determined to fight, the chances of the CSA winning its independence were remote. Overall, they did as well as could be expected given the circumstances. Same applies to Davis, though this is more arguable.
However, there are some interesting PODs to consider, all involving command changes:
1. Beauregard being put in charge of defending New Orleans. This is already being covered here:
https://www.alternatehistory.com/fo...-the-begging-of-the-acw.420338/#post-15136601
Actually it gave me the idea to post this. One thing not covered yet on the thread is that this may also butterfly away the Shiloh attack. Overall it seems to be pure upside to the CSA.
2. JE Johnston made Quartermaster General of the Confederate Army.
The CSA never really had a proper Quartermaster Department. Some of the areas that probably would have fallen under such a department, such as ordnance, were excellent, while others, like commissary, were a hopeless mess. Joseph Johnston had been Quartermaster General of the US Army right before defecting, so having him do the exact same job makes lots of sense. And it might butterfly away the dispute over rank that poisoned his relations with Davis. If he gets along tolerably with Davis, because the rank dispute is butterflied away, that means less Davis micromanagement.
This also keeps JE Johnston from field command, at least in the early years (there is the prospect of him being sent to replace the commander of one of the two armies later on). That has a lot of interesting butterfly effects. It probably costs the CSA their victory at Manassas. It may butterfly away the Peninsula campaign, which developed from a plan by McClellan to amphibiously outflank JE Johnston's position at Centerville, which McClellan thought was more formidable than it really was (but then this is a constant theme with McClellan). There is the issue of who replaces JE Johnston as commander of what became the Army of Northern Virginia. If its Beauregard, things are not that much different from OTL. If its Lee, the main effect is that Lee doesn't do his excellent work at improving the coastal defenses in the Carolinas, though probably Beauregard could have done that job.
3. Lee sent west in April 1862.
Once Lee took command of what became the Army of Northern Virginia, I think his being used in any other capacity was unlikely. But sending him elsewhere before hand is plausible. Davis used him to organize coastal defenses, which given Lee's role in the US army before the war was a smart decision, then brought him to Richmond, apparently so he could better second guess and eventually replace Joseph Johnston.
However, the battle of Shiloh took place historically almost a month before JE Johnston was wounded in Seven Pines. Davis blamed Beauregard for the defeat at Shiloh, so a POD where Lee is sent to take over what became the Army of Tennessee is plausible. Or he could replace Beauregard when the latter went on medical leave. Bragg could have been brought east to be Davis' military advisor, and probably if Lee took command of what became the Army of Tennessee he would have wanted have Bragg moved away at the earliest opportunity, their command styles were just too different.
An alternative but less likely POD is that Davis replaces AS Johnston with Lee when the Tennessee congressional delegation requested Johnston's replacement. This is a very un-Davis like move but it would have saved A.S. Johnston's life! An appropriate later role for Johnston would have been command of the Trans Mississippi Department, where he would have done a lot better than Holmes at least.
This would mean that the Army of Northern Virginia needs a commander when JE Johnston is wounded. Longstreet would have been the best choice, but I have no idea what Davis would have done in this situation.
4. The Mississippi is not a departmental boundary.
The CSA Department of the West ran from the Savannah to the Mississippi rivers. The USA put the Mississippi River valley all in one department, and had a separate department covering central Tennessee and Kentucky. Partly this was due to the USA being able to put two field armies in the West, one advancing down the Mississippi and one advancing along the Cumberland then southeast, while the Confederacy could only field one army. But adopting the US organization would have greatly improved the prospects of defending the Mississippi, as would having the Army of Tennessee defending the Mississippi instead of invading Kentucky, which would have been one likely result.
This thread assumes that the loyalties of the major ACW generals fall out as IOTL, there is another thread to cover how that would have gone differently.