One reason I can think of is too much land to control with a relatively small Army. Another reason I can think of is supplies. Northern Armies were running all over the place behind Lee. And animals; The North had a huge (more?) area for training and keeping Calvary horses. Besides an endless supply of immigrants, many who were willing to serve for a paycheck.
Or possibly, as someone said elsewhere here, the shortness of the war proved Southern Generals and Armies incompetent. The South had a small population relatively speaking. Horseman, yes, endless supply of horses, No. Other animals needed for an Army as well. Food supply was not ideal. I don't think the Confederate Generals or soldiers were inferior. Since most of the Commanders went to Military Academies, it's not realistic that they just sucked (blunt).