Good points. The south, at least at the start of the war, appeared to be much better generaled. I think it was Tecumseh Sherman who said it took their forces a few years to really get going and learn how to function and accomplish what they did in the later years of the war.The fierceness of the Confederate infantry, especially in the eastern theater, was a substantial factor prolonging the war. In shear fighting ability, they were probably better. But the US Army had a higher percentage of literate soldiers. They had a higher % of people who understood paperwork and quartermaster work. The Confederate soldiers are often described as wasteful and it was going to be a liability once they were not able to capture US quartermaster depots.
Grant put a lot of work into making his logistics based on water transport. Similarly Sherman made plans to protect his rail link to Nashville and Louisville and to be pre-stocked with rails, ties and switches, to repair bridges and tracks very quickly.
Once the Confederates were pinned down defending Richmond and Atlanta, there elan decreased considerably.