You basically said the same things I did.
Lee’s mistakes–huge in that they lost the South the war–were going on offense, twice.
Lee certainly benefited from McClellan’s stupidity, but then he also bested Hooker, Burnside, Pope. That’s a pretty good track record for someone whose military intellect you downplay. Beating McClellan alone is not a big feat, but beating the remaining of the generals tapped to lead the AoP outside of Meade and finally Grant is a pretty good record of success.
Stuart is a mixed bag for sure, but I think him a good general or at least the needle points more that way than not. Stuart became enamored with his own press I think. I can’t think of another rational explanation for the things you cite as his faults. However, Stuart did a great job of keeping the AoP from coelescing around Richmond in late 1862 into 63, so you gotta give credit there.
Gettysburg is, for me, the saddest of the battles because it need not have been a lost one. First, as I stated and I think you agreed, the battle should never have been fought. Second, Longstreet suggested on the second day, before Meade had solidified his positions on the Round Tops and along Cemetary Ridge, that Lee send his army south and around Meade positioning the ANVA between the Union and DC and on the high ground. This would have placed Lee in a defensive position and Meade would have had to attack. Instead, as Shelby Foote conveyed to us, Lee’s blood was up and he told Longstreet, “I am going to whip them here, or they are going to whip me.” Well we know what happened.
Halleck was a political general–we have many more of those today. But Grant was a drunkard. During Vicksburg, when the siege started a year (there abouts) before July 4, 1863, Grant began drinking–understandably out of boredom. Grant did not drink like that when on campaign, only during encampments or sieges. He also liked cigars, but then who doesn’t.
Ah Shiloh, how different would that battle have been had Albert Sydney Johnston not been killed in the first day. Beauregard was not a good general.