Let's suppose that Gen. Joseph E. Johnson was not hit by a chance bullet at the Battle of Seven Pines, and retains command of the Army of Northern Virginia. President Davis gives command of the Army of Mississippi in the western theater to Gen. Robert E. Lee (instead of Braxton Bragg as in OTL) after relieving Gen. P. G. T. Beauregard of command over the army after the Siege of Corinth.
With Joseph E. Johnson leading the Army of Northern Virginia in the east, and Robert E. Lee leading the Army of Mississippi in the west, how would this have affected the outcome of the war?