The major advantages of the North were that most of the manufacturing interests of the nation as well as most of the railroads were in the North. The North possessed 93 percent of the nations heavy industry; 97 per cent of its firearms, and 96 per cent of the nations railroads and railroad equipment. This not only allowed for greater manufacturing of armaments and war materiel, but also for rapid transport of troops and equipment. The North had more wagons, ships and horses, and also a surplus of wheat production which was in demand in Europe. The North had a two-to one advantage in railroad lines. Complicating this was that most lines in the South were short line runs that did not connect to main truck lines. The North had a four to one advantage in population over the South, and its government was more organized politically.
Given the advantages of the North, the outcome of the war was a foregone conclusion. The advantages of the South only allowed it to continue the war longer than anyone might otherwise have expected. Among the Southern advantages: the war was fought primarily in the South, so the South had something of a "home field advantage." Southern soldiers were by and large better marksmen than their counterparts in the North, and therefore more deadly. Finally, the South had a strong military tradition, and much better commanders. It is noteworthy that the South had only one commander in chief during the war to the North's five. That commander, Robert E. Lee, was offered command of Union forces at the outbreak of hostilities by Gen. Winfield Scott; however Lee could not bear to fight against his native Virginia, and resigned his commission. Thomas J. "Stonewall" Jackson had been professor of Geometry at Virginia Military Academy, and Pierre P.T. Beauregard had been a professor at West Point.
The South stood no chance of winning the war; but its advantages enabled it to prolong the conflict.
Likely the largest advantage that the North had, which obviously coincided with a disadvantage for the South, was the availability of supplies and the better ability to distribute them. The naval blockade of Confederate ports was obviously not 100% effective but it did reduce to a trickle the amount of supplies the South could bring in as well as completely crushing their ability to sell cotton, something they depended on for hard currency and industrial goods not widely produced in the South. So the advantage in terms of material and supplies was heavily tilted towards the North as they had far more industrial capacity and access to outside supplies from Europe and elsewhere.
The South was considered to have an advantage in the quality of their recruits as they had more experience with simply being outdoors as hunters and riders, etc. The recruits for the Union Army often needed more training and were considered inferior marskmen to their southern counterparts.
Through most of the conflict, the leadership in the South was considered more capable and certainly was more dynamic than the generals the Union Army appointed.