Lee was faced with far more challenging battles in his career than Ceasar was. Lee took a terrible scrappy army and turned it into a fighting machine that came close to turning the war around--despite the massive industrial and numerical advantages of the North. And in the end, he even secured a decent peace for his troops.
Like Miles said the confed's as a whole even before lee, had better infentry and calvery but their supply and manpower situation was terriable. That's what impresses me more about Leuage that he was able to take a small well trained group and defeat an vastilly outnumbering army, while the rest of the CSA was failing.