If Lee is alive, Lee gets the ANV command. Of the five senior generals in the entire Confederate Army: one held a purely administrative position, one was dead, one was wounded, one had feuded with President Davis, and the other was Lee.
If Lee is somehow incapacitated, after Joe Johnston and Gustavus Smith: Holmes, Huger, Magruder, and Longstreet all had Major General commissions with the same date (Oct 7, 1861). So did Stonewall Jackson.
Holmes and Huger had certain age/health issues. After Longstreet's missteps at Seven Pines vs Magruder's performance on the Peninsula, Prince John might get the command, albeit temporarily as Stonewall Jackson likely gets the permanent promotion based on his perceived performance in the Shenandoah.