As usual, I'm with Ole. Yes, A.S. Johnston was put in an impossible situation when he assumed command, and he seems to have struck virtually all of his peers as a tremendously impressive man. Nonetheless, the mistakes he made in his brief tenure strongly suggest that he was not the person who would have rescued Confederate fortunes in the West had he lived.
Thomas Lawrence Connelly's excellent Army of the Heartland: The Army of Tennessee 1861-1862, while fair to Johnston, provides a devastating critique of his lapses, both in not focusing sufficiently on the danger presented by the Cumberland-Tennessee corridor and in not fortifying Nashville. Connelly notes a tendency in Johnston to place undue reliance on untested subordinates with no follow-up.
As to Henry and Donelson, Connelly suggests that, based at Bowling Green, Johnston became fixated on the threat presented by Buell coming down overland from Louisville. He gave orders to bolster Henry and Donelson but then relied on Polk, who was fixated on the Mississippi, almost like Johnston was wishfully hoping that someone else would take care of the problem.
As for Nashville, Johnston assigned an engineer (Gilmer, the same engineer assigned to deal with the forts) to lay out defenses for the city. The engineer did so but was then unable to convince the townspeople to part with (slave) labor to construct them. Johnston never followed up. Incredibly, according to Connelly, Johnston had no idea that defenses had not been constructed until he retreated from Bowling Green to Nashville in mid-February 1862.
Although men are capable of learning from their mistakes, there is no evidence that Johnston would have radically changed or grown. If anything, the days before Shiloh, in which he delegated planning of the approach to Beauregard, seem to evince the same sort of mindset that he had displayed earlier.
I don't mean to be unfair to General Johnston. Indeed, I kind of like him and sympathize with him. He assumed a command defending a virtually indefencible line, was given no support by Richmond, and was forced to rely on the likes of George Crittenden and Felix Zollicoffer (in the east) and Leonidas Polk (in the west). (If I were a conspiracy theorist, I might think that Polk was an agent of the Union Army.) Nonetheless, the point is that the Confederacy had a very thin margin of error. The War might have proceeded quite differently, of course, had Johnston lived. (Would he have undertaken the Perryville campaign?) But I don't think he had the qualities that would have made a difference to the outcome. | 
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