Someone needs to work out in simple words how Johnston, who never had a successful campaign, nor a battle in which the enemy was damaged much, rates as a "very good general" except in the sense that the defeat was very well organized.
Governments pay generals to ensure the government survives and accomplishes its political objectives. If you want to lose with dignity, Johnson is your man. Notice how his advocates always focus on the battle he was GOING to fight, and never on the ones he actually fought?
I think the whole "army in being" thing is misleading. You can't maintain a slaveholding elite by guerilla warfare. You have to hold territory in which you can enforce law and from which you can draw manpower and supplies. This means you have to stop enemies advancing, and ideally sometimes destroy them to ramp up the cost of war. See Saratoga, Yorktown and Dien Bien Phu. Lee failed ultimately, but he was maintaining the territorial integrity of the Confederacy as far as he could, and he never lost track of needing to destroy Union armies. Johnston is the general of well-managed retreats. You maintain your army intact in order to use it, not to have a really nice-looking surrender ceremony.
Grant or Sherman over either one, but most certainly Lee before Johnston. Probably Jackson, Longsteet, Early, Gordon, Harvey Hill, Meagher and even Hood before Johnston.