Okay, in this TL I invented in about 5 seconds, for some strange reason John Reynolds is given command of the AotP after 2nd Bull Run. This post must also be read with the appropriate "tone":
The worst general in this TL, by a wide margin, is Robert E. Lee.
I mean, let's just ignore for a moment the bungling he did in 1861 in West Virginia, and the alleged incompetencies he performed while in a desk job until 1862. This is just focusing on him as an 1862 field commander.
Any fool would have known that McClellan would have run away at the sight of his own shadow. Longstreet knew it. Magruder knew it. Hill (both of them) knew it. But Lee had to attack him 7 times, 6 more than necessary, to get him to retreat. He threw away 20,000 men on the field against a mildly superior force, ignoring several possibilities for enveloping parts of the Union line, because he could not rein in his subordinates.
2nd Bull Run was won entirely because of Jackson's daring (albeit at a high blood cost) and Pope being as aggressive as McClellan was cautious. Lee just turned his subordinates loose and then lost control of events. It was dumb luck, especially with the AotP rushing northward as fast as possible.
Now, what was up with Harper's Ferry? No army in the field at that time could have executed a 5-pronged invasion with any hope of success (it was a volunteer army, people!) But Lee left his most aggressive subordinate, Jackson, in charge of 3 out of the 5 wings. That was an open invitation for Jackson to go romping around the countryside, and he still almost didn't get the garrison to surrender, with Franklin, Hooker, and Reno at his back.
And, Lee was seriously doing some very bad thinking leaving half a division (D. H. Hill) in charge of the South Mountain passes. A single Union corps could have broken through, as Franklin evidenced against McLaws farther south, but Reynolds ordered the Ist, VIth, and IXth corps forward after he captured Special Orders 191 (and again, why would Lee write that down and leave it to be found? That should have been oral orders, with one copy kept at HQ).
And finally, Antietam. What fool in his right mind would try to have an army of 30,000 men try to hold a position with no particular defensive value, their backs 1 mile to the Potomac River, against a confident, well-supplied army of size 100,000 with an aggressive commander and a copy of their exact orders? On September 15th, Jackson was still 2 days march away at Harper's Ferry, and Reynolds was not stopping his advance for nothing.
Thanks in large part to heroic stands made by Hood's and D. H. Hill's divisions in the bloody lane, no thanks to Lee at all, the AoNV managed to avoid being captured piecemeal, although 7,000 were still trapped on the north bank of the Potomac, ignoring the 13,000 casualties taken in the battle. When Jackson re-joined him Lee had about 30,000 effectives, total, versus Reynolds commanding a combined force of 120,000. And by then there was nothing preventing Richmond being captured before winter. That, with the Emancipation Proclamation issued on the 22nd, was the Confederacy's death knell.
It took until July 4th, 1863, for Vicksburg to fall, the last large Confederate Army to surrender, but after Lee's disastrous manhandling of the Army of Northern Virginia, everybody knew that it was only a matter of time.