Some background on the subject From General Longstreet's opinion in his memoirs... Lee was not a Napoleonic commander in his view (more like Wellington)... and only like Napoleon at Waterloo... It was to him Johnston who combined the art and science of war to the greatest possible degree.
General Lee:
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but General Longstreet considered Joe Johnston skilled in both the "science" and "art of war"...
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And from an 1879 interview explaining more fully his points above...
"Who do you think was the best general on the Southern side of the war?
I am inclined to think that General Joe Johnston was the ablest and most accomplished man that the Confederate armies ever produced. He never had the opportunity accorded to many others, but he showed wonderful power as a tactician and a commander. I do not think that we had his equal for handling an army and conducting a campaign.
General Lee was a great leader—wise, deep and sagacious. His moral influence was something wonderful. But he lost his poise in certain occasions. No one who is acquainted with the facts [thinks] that he would have fought the Battle of Gettysburg had he not been under great excitement, or that he would have ordered the sacrifice of Pickett and his Virginians on the day after the battle [of July 2, 1863]. He said to me afterwards, "Why didn't you stop all that thing that day?"
At the Wilderness, when our lines had been driven in and I was just getting to the field, General Lee put himself at the head of one of my brigades, and leading it into action my men pressed him back, and I said to him that if he would leave my command in my own hands I would reform the lines.
His great soul rose masterful within him when a crisis or disaster threatened. This tended to disturb his admirable equipoise. I loved General Lee as a brother while he lived, and I revere his memory. He was a great man, a born leader, a wise general, but I think Johnston was the most accomplished and capable leader that we had."