Let's get back to the original post, people.
Following the dissapointment of Murfreesboro - where the Confederates seemed on the cusp of a great victory only to end up conceeding the battlefield and retreating to Tullahoma - Braxton Bragg is heavilly criticized by his subordinates for his conduct of the battle. He becomes deeply depressed and dispondent with the lack of support he was recieving from his subordinates and, despite recieving the support from President Jefferson Davis and General Joseph Johnston - then commanding the Department of the West - he decided to step down as the Commander of the Army of Tennessee.
This leaves that Army without a commander. The only logical solution is to give the position to Joe Johnston so he will likely be given the job.
I disagree with the premise. Giving Johnston the command is certainly
a logical solution - derailed a bit by his unwillingness to assume command (as has been critically examined earlier on this thread). But IMO we are dismissing a number of other possibilities, which I now present so that they may be analyzed and shot down.
1: Beauregard.
IIRC he is next in seniority, or at least close to it. At the time he was serving as commander of the....I forget the name....the Atlantic coast department or whatever it's called. He did a very credible job defending Charleston against attack for most of 1863.
But in the grand scheme of things, given the Union's spotty track record in combined operations (some good some not so), and the overall competence of lower-level Confederate commanders, I wonder if he was being wasted in that Department. Certainly he had the rank to command the AoT, and would probably not made a total botch-up of it. Of course, his relationship with Davis was no better than Johnston's....
2: Pemberton.
Until the end of 1862 Pemberton was in charge of the same I-forget-the-darn-name Coastal Department, which Beauregard assumed command of when Pemberton went to Vicksburg. This implies that their ranks are comparable, thus their potential areas of service are comparable.
To get this to actually work would require someone else to take over at Vicksburg, perhaps Johnston in person, perhaps Beauregard, perhaps other. This being a double command-switch makes it less likely. On the other hand, A: Davis seemed to get along with Pemberton somewhat better than Johnston et al. but B: thought at least as highly of Johnston's abilities. Given that Davis was also darn obsessed with Vicksburg it stands to reason that he may put the solidly defensive Johnston in charge there and the more erratic but more offensive Pemberton in Tennessee....maybe.
3: Van Dorn et al.
Yeah those guys. Whatever happened to them after Corinth in late 1862? Because I have no idea. As an army commander, Van Dorn would also have the rank to take over the AoT, though he probably wouldn't do a very good job of it. Still, it's an option.
(By et al. I mean anyone else in Mississippi and/or Arkansas at this time, probably incompetent, who we never hear about again in the history books after Corinth and Prarie Grove, respectively)
4: Hardee or Polk
Until someone is officially named to command the AoT it will need an interim commander - most likely the ranking Corps commander (and darn it I forget which of the two it is). But why not just promote them to Army command outright with (or without) a nice Full General commission and keep the command problem localized to the AoT.
Polk, being politically crafty, would make a huge campaign for the post if it did become available. Given his friends in Richmond and everywhere he could very reasonably get it........and then run the AoT straight into the ground once 1863 heats up.
Hardee would be less likely given his impression as simply "Old Reliable", but if anyone in power in the CSA actually thinks for once (so not going to happen) he would probably be the best overall commander for the job. I cannot see him declining it if it is actually offered.
?5? - Lee
Very very difficult to pull this one off. He's available, sitting behind the Rappahannock River with his army dispersed in winter quarters and seemingly no current threat in Virginia. He has the required rank. He's a darn good prospect at this point in the war, coming off of his 1862 victory-fest.
The two hurdles are that Lee would want to stay in Virginia, and Davis would want him to stay in Virginia as well. The only way to get this to work is if every other reasonable option fails, so Johnston plus 1-4 for some reason cannot happen. At which point Davis would be forced to order Lee west, and Lee would ultimately not refuse the direct order.
In that case, expect action in both theaters quickly. Newly appointed Hooker will not wait until spring when he gets a new and seemingly inferior opponent (probably Longstreet). On the other hand Lee will almost for sure go on the offensive in Tennessee as quickly as possible. I would love to see a Lee-Rosecrans matchup in Middle Tennessee (which will of course degenerate into a Lee-Thomas matchup, which I would love even more

).