The more I read about the Civil War, the more I am convinced that the "leadership" portion is highly exaggerated, and that the success of Confederate commanders in the Eastern theater owed more to their troops being familiar with the terrain than superior leadership.
More specifically, it's telling that the Army of Northern Virginia tends to lose whenever it fights outside of its home state - often making basic navigation errors that characterize Union defeats in the same theater. Longstreet in particular wasn't very effective when he was sent West; and was essentially beaten by the much-maligned Burnside during the Knoxville campaign. By contrast Grant proved capable of handling troops in either theater.
Moreover there was an undercurrent of restraint guiding McClellan's actions - as early in the Civil War there were many in the Union who still hoped that a "silent majority" in the South would eventually rise up and overthrow the Confederacy, as evidenced by how something in the region of 100,000 Union soldiers were actually from Confederate states (which was also why the Confederates were quite ruthless about eliminating pro-Union elements in their own territory).
It wasn't until Grant that Union Army really accepted a "fight to the finish" mindset; which ironically may have been an outgrowth of Grant's experience at Shiloh. Despite winning the battle Grant was very nearly sacked anyway as public opinion was shocked by the losses he incurred - losses that turned out to be the norm for Civil War battle rather than the exception.
If you want to press home the idea the South had no interest in making war on the North by merely defending their borders, you are correct.
However, at the outbreak of the war, the South has professional generals whereas the North frequently makes due with political appointees.
Stonewall Jackson is in possession of a massive map of the Shenandoah Valley marking every road, mountain pass, forest trail, and river ford known. He combines what with very effective training for his 'Foot Cavalry', he puts them in places where they can win until their elan is elite, and he uses speed and knowledge to show up in places he cannot be.
This is not leadership?