I never said Shiloh wasn't a Union victory. Just that Grant lost horribly until his vast reinforcements came. Petersburg was so defended BECAUSE LEE CREATED ALL OF THE DEFENSES. Seriously. Do you think they materialized out of thin air? You also say that he outnumber Lee 'less than 2:1', as if it's some sort of big achievement that he won because it wasn't quite 2 to 1. I had forgotten about Vicksburg, which was certainly a great campaign. But you either forget about or purposely ignore the Second Manassas campaign, the Chancellorville campaign, the Sharpsburg Campaign(in which he captured the extremely well defended stronghold of Harper's Ferry with a small, outnumbered contingent of his force and drew an army over twice the size of his own before withdrawing at night and smashing McClellan at Shepherdstown), and the Wilderness(in which he was outnumbered 2:1, and still repulsed Grant's army from pushing forward to Richmond, nearly cutting odd the entire offensive). Those are only Lee's best. Vicksburg was undoubtedly the best Union campaign. Compare that to Jackson's Shenendoah campaign. There's no competition.
While I shall agree that Second Bull Run was very impressive, I shall point out that Lee's performance in the Maryland campaign was quite poor. When Lee divided his army, the force that seized Harper's Ferry was not outnumbered by the garrison, it outnumbered the garrison. About 30,000 rebels against 17,000 Union soldiers. Secondly, the seizure of Harper's Ferry was not very impressive, it was ground that would require an immense garrison to defend the three mountains. Frankly, I could have seized Harper's Ferry with 30,000 men.
Another failure of Lee was his decision to divide his army. Both Longstreet and Jackson opposed the idea of dividing the Army of Northern Virginia into five parts and using 3/5 of it to capture Harper's Ferry. Lee splitting his army into five pieces nearly enabled the destruction of each of those pieces in detail; in fact, Union VI Corps commander William Franklin seized Crampton's Gap, and was poised to crush at least one of Jackson's divisions and save Harper's Ferry, but he managed to convince himself he was outnumbered instead. Instead of splitting his army, he should have taken up position at South Mountain and from there smash McClellan.
Lastly, the battle of Antietam itself is a mistake. When McClellan cornered the rest of Lee's army at Sharpsburg, where, thanks to Lee failing to take use of McClellan's hesitation to withdraw, he risked having most of his army destroyed. With a inferior force, he fought on a battlefield where he had one relatively easily interrupted escape route if he lost.
Vicksburg and Shenendoah campaign? You're right, there is no competition. Grant's Vicksburg campaign was by far the superior campaign.
Strategically, the Vicksburg campaign bagged 30,000 men of the Confederacy and split the CSA in half. In comparison, Jackson drew off Union men that could have been sent to Richmond.
In terms of logistics, Grant cut himself off his supply lines and operated in hostile territory. Jackson in the meanwhile operated in friendly territory.