There is no simplistic reason for history, it is made up of a combination of factors, personalities, circumstances and manipulation and is always clouded by emotion.
One truth we should be able to agree on about the Civil War is that the great generals of both sides were Americans. They were not somehow all born Rebels that appeared out of the southern soil. They were products of the West Point!
VMI was not established to supply leaders for the Confederacy, it's graduates for all of it's history except for a short period between 1860 and 1865 have served the US. Therefore I find it ridicules to claim the US didn't produce a good military commanders for the first few years of the Civil War. The US produced all the great Generals of the Civil War!
Lee did not attend West Point with the intention of leading the ANV! He was every bit as much an American as was Grant. This is something it seems all Civil War "nuts" of today have forgotten.
The next great truth that we should be able to agree on is that at the beginning of the war both armies were comprised of little more then armed mobs. Neither side had an advantage, neither side had the ability to force the other into submission of the others will. Every soldier involved in those early battles were Americans! This idea that there was somehow two separate nations sharing one common federal government is totally bogus. Every law passed between George Washington's administration and Buchanan's was influenced as much by Southern states as by their Northern counter parts. The way some people act you would think the Southern states had been forced into the US against their will. Bogus again! They were instrumental in the founding of the US and in fact produced 15 Presidents including Washington, Jefferson, Madison, Monroe, Harrison, Tyler, Taylor (all Virginians).
Until the late 1840's the Senate was controlled by slave states. So lets start this discussion from the understanding that the South was and remains as much a part of the US as it has since the beginning of our revolution.
In the early years of the Civil War both sides suffered from the plague of "political military commissions" much to the dismay of Lee in the South and Grant in the North. Grant was not a unknown person in military circles (which was a very small circle in 1860). Longstreet knew him very well, was his best man if I recall, and had introduced young Grant to his cousin one Miss. Dent. whom he married, and had even advise others on Lee's staff when word that Lincoln had appointed Grant to lead the AoP that he would fight them at every turn.
Grant openly wept when news of the deaths of Confederate leaders he knew well reached him. These men that were produced by the small and elite military academes in the small nation that we were then, were members of a small fraternity. There was little chance of advance to higher rank in the US Army that Grant had resigned from earlier. With only 16,000 men serving in 1858, most of them stationed in the western frontier, the chances of advancement had little to do with ability, but more from opportunity and the inevitable political gamesmanship that plague the military institutions of the time.
However, upon secession the states that formed the CSA lost the resource of West Point, the North did not. West Point continued to supply the North with young officers to replace those that were lost during the war. The South had to depend more and more on promotion of those who either had political influence and very little military knowledge, or were promoted from the rank and file. If the South had an early advantage from experienced leadership it quickly evaporated. The CSA in general suffered more from the lack of institutional and bureaucratic infrastructure through out the war. The South just didn't have the overall co-ordination the North enjoyed. The departments of procurement and command cohesiveness was lacking, as Davis told one newspaper man early in 1861 when asked about the CSA'a state department, "I keep it under my hat" as he pointed to his head gear. When the Davis administration relocated to Richmond the little town of 37,910 grew to 125,000 by 1863. Those seeking political power and offices bloated and overwhelmed it's resources. When the war was over the political hacks and hustlers quickly abandoned the CSA's capital city and by 1870 it had shrank to 70,000. DC also under went great pressure from expansion but the government agencies needed had been in existence and were already functioning, they were forced to expand, the CSA had to create them out of thin air, at the same time it was creating a Navy and a Army and doing so with out the same support for a federal style central government as existed in the North.
So who had the early advantage?