Did Lee not have any responsibility in choosing his corps commanders? Or in communicating his orders to them, such as they were understood? Or removing them from command if necessary?
The commander bears ultimate responsibility, that is true, but adhering too closely to the principle makes real analysis impossible. It is rarely so black and white.
Let's look at the three examples given:
1. Stuart leaving Lee blind by going on a joy ride to soothe his ego. It's possible Lee could/should have foreseen this but it is not really something anyone should be blamed for not foreseeing. Stuart had been excellent in his role to that point. There was no reason to relieve him or to suspect that he would be less than excellent during the campaign.
2. Lee's health. I'm not sure this was really an issue, but if it was, it certainly isn't something to blame Lee for except perhaps if it were to the point that Lee should have stepped down. It wasn't, so he didn't, and if it was, then it was really on Davis to have him temporarily replaced, at least by the reasoning you present here.
3. Ewell's failure to take Culp's Hill and Cemetery Hill on day 1. This is the one for which Lee bears the most responsibility, I think, though Ewell does, too. Lee was not emphatic enough in defining the specific thing he wanted accomplished. His addition of "if practicable" to his order to Ewell gave Ewell the leeway not to carry through. In the past, such a gentlemanly wording had worked to spur action with all effort, and Ewell's performance to date since taking over Jackson's corps had indicated he would need no more than that.
But it didn't work. Ewell decided it wasn't practicable so he did not attack. One can blame Lee or one call Ewell too timid.
Or one can reasonably question whether such an attack would have been successful at all. Ewell had already lost a few thousand men in the day's fighting, and the remainder of his Corps was disorganized from the pursuit through the streets of Gettysburg. More importantly, Hancock had already begun digging in on the heights; fortifications were springing up, and there were nearly 40 cannon in place on the heights by the time Lee's order came. Had Ewell attacked, it is a reasonable possibility that rather than taking the heights he would have had the remainder of his Corps shattered.
Then, of course, is Longstreet's mishandling of the approach to his assault on the Union's left flank on the second day. I wouldn't blame Lee for that, either.
Sorry. Long-winded.
TL;DR version: Much of what went wrong really can't be laid at Lee's feet, at least not directly, and some things that were said to have gone wrong really might not have been wrong after all.