Sidney's record is at best a might-have-been fantasy (even more than Joe's) and at worst an actual example of pretty consistent failure.
Even allowing for all the difficulties he faced, he did not handle the situation - such as for instance the issue of whether the Tennessee was defended - very well.
Yeah, basicly he didn't check out the Forts Henry and Donelson to make sure they were well situated, built and supplied. He then gives the command to Floyd who was a political general with no military experience. Floyd attempts to counterattack Grant and then orders his men back to the trenches the moment things go wrong even though they made a partial breakthrough. If Floyd pressed on he probably would have escaped with at least some of his men. After this Floyd surrenders the next day despite being in a fortress. Then came Shiloh where he disregarded Beauregard's advice of not fighting there. Instead of bypassing a sunken road which was a good defensive position for the Union he assaults it at least 8 times. He then dies by leading a charge which is not the job of a full general.
Yes, A.S. Johnston is massively overrated. His strategic missteps in early 1862 basically cost the Confederacy that part of Kentucky which it held as well as West and most of Central Tennessee.
I think his career was too short to really know what kind of general he would have been in the long run, if he had survived. Most of the generals had a "learning curve" at the beginning of the war and made mistakes of one sort or another. After all, just about all of these guys were men who had, at most, led a regiment (or in some rare cases, A.S. Johnston included, an ad hoc brigade) prior to the war, and found themselves in command of armies made up of equally inexperienced subordinate commanders and raw recruits. Johnston fared worse in that regard than the commanders in Virginia did...it is a fact that the main army in Virginia pretty much got the cream of the crop in men, equipment, and officers, with whatever was left over going to Johnston in the west.
Johnston was also handicapped in that was essentially given an impossible task. He was given a front stretching for several hundred miles to defend with a force about the same size as that defending northern Virginia. The very size of the area he was assigned to defend made it basically impossible for him to personally visit every post within that territory...or even all of the most important ones. Remember, most of these places weren't connected to rail lines, which means days or weeks in the saddle to get to them. He was basically forced to delegate large responsibilities to subordinate commanders who proved not to be up to the task. Thus you had situations like Forts Henry and Donelson (incidentally, John Floyd DID have military experience, having commanded in the Mexican War. He had also served as Secretary of War. He thus had a reputation for knowledge of military affairs which was, as it turned out, completely undeserved).
As for Shiloh, Beauregard screwed that up, not Johnston. Johnston had designed a plan of attack which could very well have avoided most of the pitfalls which plagued the Confederate assault on the first day. Beauregard instead substituted a plan of his own which was overly complex and which ensured that units would become mixed up in the wooded terrain and that commanders on the field would not be able to retain control of their troops. Beauregard's adjutant, Colonel Jordan, also screwed up the plans for the march from Corinth to Shiloh, which caused the Confederates to arrive there 1-2 days later than they would have if Old Borry and his adjutant hadn't been there. If the battle had been fought 1-2 days earlier, as Johnston intended, Buell's Army of the Ohio would not have been close enough to intervene. And yes, the Hornet's nest was a mistake, seen in retrospect. However, it would have been considered sound military tactics by the standards of the day, which dictated that one did not leave fortresses in one's rear. The Hornet's Nest was essentially a fortress from which the Yankees could have mounted an attack on Johnston's exposed flank or rear if he had bypassed it. "Infiltration" tactics where one bypasses strongpoints and exploits weak places in the enemy lines didn't come around until World War One.
I don't know that Johnston would have proved to be a great general if he had survived Shiloh. We really don't know because he was killed so early in the war. I can't help thinking that he would have turned out better than Braxton Bragg, though.