Most accounts of Albert Sidney Johnston indicate he was held in much higher regard as an officer and leader of men than Robert E. Lee, who has become the more iconic Confederate general.
Winfield Scott called Johnston a "Godsend to the Army and to the country."
Jefferson Davis wrote: "I hoped and expected that I had others who would prove generals, but I knew I had one, and that was Sidney Johnston."
Meanwhile, R.E. Lee was criticized for his incompetence in western Virginia (soon to become West Virginia) during the opening weeks and months of the war.
By late 1861, Johnston was thought to be the Confederacy's "finest soldier."
If that's the case, then why the hell would Jefferson Davis and the Confederates send Johnston to the Western Theater? The West was a mess, yes, but I would argue Virginia was more important for the Confederacy's survival. Therefore, Albert Sidney Johnston should have been commander of the Army of Northern Virginia and Lee or Joe (the other) Johnston sent West. By sending Albert Sidney Johnston to the West, the Confederates effectively shot themselves in the foot.
I'm not trying to argue that Johnston was a better general than Lee. I don't think Johnston ever got much of a chance - he was killed in 1862, after all. So naturally Lee is the Confederate hero of the history books, and well deserved. I do in fact think Lee was the superior leader in the end, but mostly because Johnston was killed so early on. Jefferson Davis' 1861 decision to send Johnston out West is, to me, one of the worst decisions made by either side during the war.
So do we have any idea what kind of thinking went into that decision? Why did it make sense at the time?
I waited long enough for a real historian but none showed up. The question implies that the Eastern Theater was indeed more important. However that was not the approach of Jefferson Davis. Steven E. Woodworth describes the first military doctrine of the Confederacy in his 'Jefferson Davis and his generals: the failure of Confederate command in the West'. It was a 'we defende every inch of our territory everywhere' approach. That does not emphasise the importance of the Eastern Theater - au contraire, it emphasise that the Western Theater is just as important.
Second of all, by the time Johnston returns from California the Easter Theater is more or less secured by the Battle of Bull Run. However there is only a black hole of nothing on the Western Theater. With the collapse of the Kentucky neutrality the war spread out to the vast region from the Alleghany mountains to the Mississippi and Missouri was already fighting. If an experienced and energetic leader was needed at the time then it was needed on the Western Theater.
Moreover the victory at Bull Run made the public excited and euphorical. There was no way to relieve the two generals who successfully concentrated and fought at Bull Run for Davis although he very much desired to get rid of them. They were just promoted to full general in July 21. But the bigger threat came from West at the time.