Say during the Battle of Shiloh, Johnston's injury simply never happens. Does he go on to win the battle? And what affect does his survival have on the course of the Civil War?
I am going to give a minority opinion on this and say that I don't think it changes anything. I know ASJ was seen as a brilliant commander, but I just don't see it. I think a lot of his contemporaries have used ASJ to throw shade on other Confed generals, praising him to criticize others. Jefferson Davis in particular seemed to have used ASJ to dump on Beauregard, for a variety of reasons.
Here is my problem with ASJ (well, besides him being on the wrong side of history and fighting for a vile cause of treason and slavery), everyone talks of his potential. No one talks of what he did. He looked like a general (over six feet tall, broad shoulders, big chest, acted dignified and serious), so everyone assumed he was a great general. People called him a genius, but no one could name a single genius thing he did.
T. Harry Williams put it far better than I could, but here is the other problem with ASJ, the things he did were puzzling and did not show promise. He commanded a line of troops from Arkansas to Bowling Green, Kentucky. East of Mississippi, he had 48,000 men holding down 150 miles. West of Mississippi he had 22,000 men under Van Dorn. He stationed himself... in Bowling Kentucky. The extreme right flank of his army's position. Where he reduced himself to being a commander of 14,000 men stationed in town... instead of bothering to run an army of 70,000 men that reported to him. Red flag.
Next, opposing him north of Bowling Green was Buell with 70,000 Federals. Western Kentucky had Grant with 20,000 men. Missouri had Halleck with about 30,000. So, ASJ has a numerically inferior force. And yet, in Bowling Green and Columbus, his two flanks East of Mississippi were salients jutting out ahead of Fort Henry and Donelson. He was operating outside of a circle. Red flag.
Oh and the two forts were on two rivers, Tennessee and Cumberland, flowing into Ohio. If the Federals, using their superior naval strength could seize the forts, they would be between the Confed forces on the flanks and attack either flank at will. Red flag.
Grant takes Fort Henry. Hardee and Beau (stricken with a bad throat after a surgery) discuss this and realize the obvious next target - Donelson. The plan is to defend it. Hardee takes it to ASJ, who decides they must fall back on Nashville, abandoning Donelson and splitting his army (east of Mississippi) due to an error of his own making and having them retreat separately. Red flag. Before he does so, he (ASJ) writes a memorandum and makes Hardee and Beau sign it, saying Donelson must be abandoned. Hmm? Okay.
ASJ refuses to let anyone lead the 14,000 men out of Bowling Green. He chose to lead them out himself. Why? Then, having gone on record to Richmond that Donelson cannot be held, nor taken, nor re-taken, he sends 12,000 men to reinforce it (!). The Hell?