A war has proven to be a matter more complex than just armies fighting each other. In order to win a war you need several elements other than just military might. You need massive, overwhelming popular support, you need numerical superiority, you need a solid and robust industrial sector that can produce all the military and other related supplies to both the military and the civilian population in the home front, you need great leader with a special combination of vision, idealism and pragmatism, you need allies and you need the best technology you can have.
The South was deficient in many of these elements:
The Union had 27 million men in the Army against 7 million Southern army regulars. Unless you have weapons of mass destruction that allow you to eliminate the enemy’s surplus of men you are not going to be able to overcome such a massive difference or at least not that easily.
The defense of the Union enjoyed massive moral support grounded in solid moral principles: a rejection of slavery, the fact that the South attacked the North first and the defense of the America that the Founding Fathers had created. The South was utterly divided, rich planters with slaves fully supported the war effort but they only had money, not men and their black slaves were certainly not going to fight to maintain slavery. Southern poor yeoman farmers did not care about slavery and when their sons got conscripted and killed to fight for the riches of wealthy Southern slave planters and their crops were seized they either rebelled or helped union spies or southern deserters. Even the State of Virginia was divided, since the Western part of it refused to secede.
The North was heavily industrialized and was able to mass produce weapons and engines of all kinds in order to support the war effort. The South had barely any industry and was unable to import weapons massively enough to equal the Union’s firepower.
Lincoln was an admired leader of solid moral principles and impressive mental and interpersonal talents. He was able to keep the Union focused and united and motivated. Jefferson Davis was an autocratic, disrespected arriviste who did not command the same loyalty or devotion.
The North had allies like Canada and even Tsarist Russia to some extent and was able to ensure the other European powerful nations remained neutral. The South was completely isolated with the exception of Britain that did try to help them a bit but British public opinion was massively against slavery and that prompted their government to stay out of the War. Monarchic France was also somewhat sympathetic to the South but was more concerned about their imperial plans in Mexico.
Because the South had invested little in education and research, the North surpassed it easily in that as well.
They did have most of West Point graduates, but only Lee was a remarkable general. They did have less soldiers but very motivated ones. They were able to put up a great fight and for two years they kept winning. But the Union persisted and they could only prevail. The South was never going to win.