This ACW scenario, for a change, is about the U.S. war effort doing better than in real life, rather than worse. Namely - Let's say that Grant takes more defensive precautions before the battle of Shiloh, rather than being caught completely unprepared by A. S. Johnston. As a result, rather than overrunning part of Grant's forces and pushing them back the attack stalls early on. (Johnston, who was ridiculously foolhardy, still wants to lead from the front lines and still gets shot). The casualty totals are somewhat better for the Union and Buell isn't as necessary. This means that Grant doesn't get quite the wave of bad publicity and reputation for being a butcher that he got in real life. As a result, two months later when Lincoln is looking for a hard-driving western general to come to Virginia, Grant gets the nod rather than John Pope.
So, how is Grant likely to do commanding the Army of Virginia against Lee? Also, in Grant's absence, how well will Pope and Buell handle the western theater?