A. S. Johnston had a good reputation, but it wasn't really based on much. His strategic decisions leading up to Shiloh were usually wrong. He obsessed about the defense of Bowling Green, ignoring Union threats on his western and eastern flanks. When he decided (too late) to send reinforcements to Fort Donelson, he sent a force too small to save the fort yet too large for him to afford to lose; it also never occured to him to go there himself and take personal command. And when the fort fell, he clearly panicked, made no attempt to defend Nashville, and abandoned vast amounts of supplies that the Confederates couldn't afford to lose.
He displayed a frustrating lack of attention to detail, assuming that his subordinates were always doing what they had been told to do and not keeping a close eye on them. He assumed, for example, that both Fort Henry and Fort Donelson were complete and ready, when in fact neither was in a state fit for proper defense.
It's impossible to say what A. S. Johnston might have achieved had he survived Shiloh. He may have come into his own, learned from his mistakes, and been a good commander. But truthfully, his record up to Shiloh is not encouraging.