The Northern states had a huge inbuilt advantage over the South from the very start. Their final victory was virtually inevitable before the first shot had even been fired. For one thing, the North already had the relevant governmental institutions and economic infrastructure in place to wage what was effectively the first modern war. As well as having an economy that was over-reliant on agriculture, the South had to build a new system of government from scratch.
The Confederate States of America was based to a large extent on the weak, unwieldy Articles of Confederation that had existed before the Constitution. That particular arrangement had helped the American colonists win the Revolutionary War, and doubtless many Southerners saw no reason why a similar arrangement couldn't do the same for them in their conflict with the North. Unfortunately, the Articles had proved incapable of establishing the United States as a strong independent nation, ready to take its place in the world. Yet this was the system on which the Confederacy was largely based.
The Confederate government often found itself frustrated in its attempts to requisition men and resources from the individual states, who wouldn't accept encroachments on their rights from the authorities in Richmond any more than they would from Washington. In fighting the Civil War, the Confederates believed that they were also fighting for states' rights, and yet it was that very same principle which made it hard for the South to wage war effectively.
Bizarre as it may seem, the states were hostile towards any attempt by the government in Richmond to institute conscription. To them, it was a sign of despotism, an attack upon the republican system of government. Just as the American colonists had resisted the British, and just as the South had resisted what they saw as the tyranny of Lincoln, so too would the states resist what they perceived as attacks upon their ancient liberties by the authorities in Richmond.
In some respects, then, the South's defeat in 1865 represented in military terms what had happened politically in Philadelphia back in 1787—the triumph of strong, centralized Federal government over states' rights and radical republicanism.