I had a silly thought. What if McClellan and Lee switch places?
I know Lee went with Virginia when it rebelled; What if he stayed with the North?
I know McClellan knew how to train men really well, just not how to use them aggressively; But that's all I know about him. I can't think of any references about loyalty with regards to him.
McClellan was true Blue through and through. So, despite what in modern lights are some of his political short commings, it'd be ASB for this Pennsylvanian to join the rebellion. However, if we handwave or TL them away, I could see a McClellan type character doing quite well in the Eastern Theater for the Confederacy.
A more fluid gurilla type might be necessary for Confederate victory in the West, but even a McClellan in the West would probably buy the Confederates at least a couple of months if not a year against Union advances there, since no doubt all battles would be on the defensive, will well placed artillery and dug in troops, even if against vastly superior and more mobile union forces.
And, one advantage McClellan 'mentality' southerner might have is that he he probably wouldn't surrender like Lee, if and when conventional resistence became impossible. Again, despite his limitations, he was more of a romantic than Lee overall I believe. At least, had he been a Southern, I think he'd been less inclined to 'survive' the war, despite his timidity. At least if you can count his letters to his wife for anything. Which could have massive butterflies for a gurilla resistance.
Either way, with McClellan, or a McClellan type in Command of rebel forces, there's definately no Invasions of the North. And while there's probably no Lee drive of the Federals out of Northern Virgina, Richmons to Petersburg, to the West probably become trench warfare earlier. And the South probably has the men to man those trenches for a lot longer than OTL. (And more resources for building ironclads, ect. to challenge the blockade.)