Obviously from a historical standpoint, the United States of America had the most advantage, as having more advantages typically mean that that group will win. The United States simply had much more advantages then the CSA:
1) The United States had a much larger population in which they can draft soldiers. The CSA has over 10 million less people, and many of the population counted are slaves (see the 3/5th compromise, which states that out of every slave counts as 3/5th of a legal person, which gives more overall population, and therefore, more seats to southern states).
2) The North had already been industrializing (due to the harsher climates in the North which created an environment that was not profitable to grow crops). The South, on the other hand, had little factories, and relied heavily on trade to procure resources, as many used the advantages of better farming environments to grow cash crops.
3) While the CSA had many experienced officers (who typically left to defend their homes from the US army), the US army was much more bigger, and this factor alone allowed the US to be able to take more casualties and sustain the army strength, while casualties towards the CSA would be more hard hitting.
4) The US is already acknowledged as a nation, while the CSA was on. Because of this the US had much more weight in foreign affairs, and was mostly able to keep foreign interests from helping the CSA. On the other hand, the CSA desperately sought for foreign recognition in hopes to gain foreign support through either loans, mercenaries, or other support.
5) Most of the fighting occurred in the South (except for the battle of Antietam, as well as the battle of Gettysburg). The battle of Bull Run occurred near the US capitol, however, it was still located in Virginia, a Confederate state. This allowed for most of the US infrastructures to be untouched, and production stayed fairly stable, while the CSA suffered large amounts of damage to their populated cities, crops in the field, which led to less war material for the army, as well as food in general.
There are many more advantages that the US had over the Confederates.
The only counterarguments that the CSA had over the US was simply two valid points:
1) Many of the southern experienced officers left the US army to join the CSA, and with that, brought many of their experiences, which led to their early success.
2) Most of the fighting occurred in the South, in which the South knew the terrain much more better, and was generally able to choose more favorable positions for the fight. However, this proved to be a double edged sword.