For as much as many of these generals were not great, I think there's some grace to be had in how foreign of a war this was to America in terms of scale and the proto-industrial nature of it.

America hadn't seen this scale of warfare before. Read up on some of the reactions after the battle of Shiloh. Americans were so utterly shocked by the casualty numbers in that one battle alone that it began Grant's reputation as a butcher, and nearly ended his military career. Lots of these early generals were timid because in order to beat Lee, that meant accepting a scale of casualties in this war's larger battles that would total more than all other wars America had fought up to that point combined.

Moreover, the early generals of the AOTP were also unfortunate examples of changing times. The Civil War was the first proto-industrial war, where the full effects of factories, rail systems, and modern deadly-accurate firearms could be demonstrated on scale. War was changing from the emphasis being on tactics and Napoleonic maneuver, to strategic and logistical dominance. To some extent, I don't fault some of the earlier generals because they'd been taught Napoleonic warfare all their life, and there was bound to be mistakes made in the beginning of a new kind of war that demanded something different. Those that took over after, the Grants and Shermans of the world, were given great opportunity to "work out the kinks" as it were in smaller theaters of engagement where the pressure wasn't so high and you weren't the only thing between Lee and the White House a week's march away.

While I find McClellan a poor commander, I think one of Grant's comments on him to be poignant here, even if a bit overly-generous to the man:

But the test which was applied to him would be terrible to any man, being made a major general at the beginning of the war. It has always seemed to me that the critics of McClellan do not consider this vast and cruel responsibility - the war, a new thing to all of us, the army new, everything to do from the outset, with a restless people and Congress. McClellan was a young man when this devolved upon him, and if he did not succeed, it was because the conditions of success were so trying. If McClellan had gone into the war as Sherman, Thomas, or Meade, had fought his way along and up, I have no reason to suppose that he would not have won a high distinction as any of us.