I”m going to say Kirby Smith. Here's why...
--Sidney Johnston gets a lot of credit that I am not sure he really deserves. Yes, Jefferson Davis thought he was the best General the South had. But his record is decidedly unimpressive. His original plan at Shiloh was a good one, and if it had not been screwed up by Beauregard, might have won him a decisive victory. But he allowed Beauregard to screw it up...he was in overall command of the Army. And he never actually WON a battle or a campaign while in command. So I can't with all honesty say he was the best. At most, I can say, we really don't know because he was killed so early on.
Not going to argue with this. A.S. Johnston had some potential but he allowed himself to get carried away with the fighting in the first major battle he fought and left the more important job, the one he should have been doing, to Beauregard and thus he lost control. The fact that we can only speculate about what he could have done makes him more a unknown factor than great.
--Beauregard screwed up Johnston’s plan at Shiloh. ‘Nuff said. He never really performed well out west at all (his biggest achievements were in defending Charleston in 1863-64 and at Petersburg in 1864).
I get the feeling that Ol' Bory wasn't that comfortable out west. It was probably the shere size of the theater that worked against him. As he proved in the Bermuda Hundred he a damned good general in a constrictive theater but I think that the West was too large for him to handle. One of the major mistakes of the Confederacy however, in my opinion, was t give Pemberton command in Vicksburg in stead of Beauregard. The defense of Vicksburg was a job that suited him.
--Braxton Bragg. The less said about him, the better. A total disaster.
Bragg was more a disaster for his personal relationships that his military ability. I agree that he should never have been an Army Commander because he wasn't cut out for the job both personally and professionally but he would have made a good corps commanders, like Hardee. If he hadn't been such a bitter, vendetta machine that targeted friend and foe alike he might have been an average Army commander but he was a total disaster in stead.
--Earl Van Dorn: Was a decent cavalry commander, but never did well in charge of an Army, either at Pea Ridge or at Corinth.
Van Dorn was arguably one of the few Generals in a role that suited him in early 1863. Being in command of a Cavalry force in Tennessee he had hindered Grant's advance on Vicksburg and was a major threat but I agree that he was a poor Army commander. He only got the job in the first place because Henry Heth and Braxton Bragg had turned it down.
--John Pemberton was pretty much a disaster too. Refused to cooperate with other Confederate commanders, lost Vicksburg.
Unfortunately for Pemberton he was simply too good at military politics. He knew who to suck up to and when and because of this he was promoted beyond his level of compitence. He would have made somebody a good chief of staff but a field commander he was not.
--Joe Johnston would be my second choice, but although he probably had the right idea for a war-winning strategy for the Confederacy, in the end, all he ended up doing was exhausting the patience of the government he served, and having himself relieved, leading to the loss of Atlanta and the re-election of Lincoln. He also did fairly poorly during the Vicksburg campaign, not using authority he clearly had to get the various Confederate forces working together.
Johnston had a lot of theoretical power in the Vicksburg Campaign but Pembeton had all the actual power. Johnston sent Permberton three direct order in the Vicksburg Campaign. The first was to march east, attack the Federal at Clinton and break through to link up with Johnston's forces. The second was to march northeast and link up with Johnston's forces at Canton and the last was to save the Army and not retreat with it into Vicksburg.
Pemberton said he would follow Johnston's first order but ignored it and marches
South. He obeyed Johnston's second order but unfortunately a spy had told the Federals of it and Pemberton was caught and defeatedat Champion Hill. He ignored Johnston third order and withdrew into Vicksburg with all of the Army of Mississippi save Loring's division.
Johnston would have been within his right to berate Pemberton for disregarding his order twice but he did not. In stead he tried to rescue Pemberotn but could not build an Army fast enough.
Pemberton gets a bit of a free ride in this because people blameh is poor dicisions on Davis or blame everthing on Johnston for not trying to break the seige of Vicksburg but Pemberton ignored direct orders from his superior in the theater twice and then blamed Johnston for everything.
Though Johnston theoretically had the power to order everyone in Mississippi around the fact thet he only had an immediate force of 6,000 upon arriving left the actual power in Pemberton's hands, Pemberton controling the bulk of the manpower.
--John Bell Hood, I think, has gained a worse reputation than he deserves. His battle plans during the Atlanta campaign were sound, but implementation by his subordinates was poor. His move against John Schofield’s Union army at Spring Hill, Tennessee was absolutely brilliant, and could have resulted in an amazing victory if it had been properly carried out. Once again, his subordinates failed him. The one major personal failure for which he can be blamed…and it was a doozy…was ordering the attack at Franklin which pretty much destroyed the Army of Tennessee. That was a fit of pique on Hood’s part, and inexcusable.
I think part of Hood's problem is that he doesn't know what to do with his army one battle has begun. He can devise good plans and get his army to move very quickly but once battle begins he's a slogger. Once battle begins the only thing Hood thinks of is finding the enemy and engaging the enemy whenever and wherever they are.
Typical of a Hood offensive if Kolb's Farm in the Atlanta Campaign. Hood had been moved there to shift the strength of the Army of Tennessee to where Johnston expected an assault but Hood saw the enemy and engaged. He drove some pickets from the field then met the entrenched Army of the Ohio and launch a number of bloody frontal assualt before calling it a day and declaring a victory won.
--Kirby Smith, with minimal men and resources, pretty much handed defeat after defeat to the Union forces in the Trans-Mississippi west, despite being heavily outnumbered (much more so than the armies east of the Mississippi). He, along with Richard Taylor, came close to destroying Banks’ army in the Red River Campaign, and right up to the end, most of Louisiana, almost all of Texas (the Union had small enclaves at El Paso and Brownsville), and a good chunk of Arkansas remained under Confederate control. One has to wonder what he might have done at the head of the Army of Tennessee.
I agree that Kriby Smith was quite good commander but his problem was he was bad at military politics. Once he turned on Bragg that was his tenure in the major theaters over. He was, in my opinion, one of the few men actually suited for Department command as well as Army command. He's quite underrated in my opinion, generally speaking, but I still dont rate him above Joe Johnston.