I agree that splitting the West into multiple departments could make things worse for the South given Davis' propensities. You seem to think that I am trying to act as an advocate for the South, trying to think of things that will make things better for them. Some of y'all are acting as advocates one way or the other, but I'm not. I'm just trying to take the POD seriously and game out what will happen.
Of course Davis will give Johnston an important position. That's not the point. The point is that y'all are assuming that given a pretty major theater-shifting POD, the appointment of generals will go almost exactly as in OTL. That's nuts. In OTL, Davis would have appointed Johnston to command of the Army of N. Va. if he could have, but Johnston got on the scene too late. The same dynamic might play out in TTL. What Davis wants to do isn't the only factor, even for Davis.
I don't think it's nuts to assume that if General McClellan becomes general-in-chief he'd still be recalled to go to Washington, while Generals Halleck and Buell receive their OTL Departmental Boundaries. If anything, given McClellan liked Buell I could see the Army of the Ohio benefiting greatly from that friendship in this specific scenario, while the Army of the Potomac still needs to defend Washington, DC, and capture the major logistical and industrial center that is Richmond, Virginia.
The need to defend Washington will remain consistent no matter how things operate in the West, and Halleck and Buell will still outrank the later generals who actually won the war. It is extremely unlikely for the first major offensive in Virginia to turn into a decisive victory for either side, and that in turn means that the Confederacy will start the war better able to menace Washington than the USA can menace Chattanooga/Atlanta.
However in this case, Lincoln's goal of capturing East Tennessee jives with overall US strategy, and Buell, a very Halleck type of general if a bit more inclined to actually fight, has his own Grant in one George Thomas, the best defensive general on either side and a sledgehammerer (by comparison Grant is a jackhammerer) on offense. So Buell's career might reflect that of Henry Halleck and George Thomas might end up taking over Grant's role, with fewer overall battles but much more decisive characteristics in the short term to those battles.