One reason, as James McPherson points out in This Might Scourge is that unlike most rebellions or civil wars, the South occupied nearly 100% of the territory it hoped to hold on to at the outset of the war. If you actually look at the strategy and tactics of the war, excepting a few ill-fated invasions by Robert E. Lee, the North basically had to re-take the South inch by inch. That takes a lot of time, even with superior resources. Add on to this a handful of dithering Union generals, political infighting and a reluctance for total war on the part of the North, it took even longer until Grant and Sherman were really freed up and empowered to deploy the strategies they ultimately used to win the war.