Almost none. As historian (and Mississippi native) Shelby Foote liked to say, the North fought the Civil War with one hand behind their back.
My reckoning, here are the advantages the North had:
--More good senior officers from the regular army. Oh, I know, the traditional wisdom is that the South got the better of the deal. Well, Lee and Cleburne were the only senior officers from the Regular Army that went for the Confederacy that a consensus would say were outstanding. Maybe you can include Longstreet (although he was unimpressive when he faced better Union leaders in the West). Meanwhile, the North inherited: Thomas, Sherman, Hancock, Sheridan, Reynolds (who peers regarded as Lee's equal tactically, intellectually and as a leader), Wallace, Sedgwick and Meade. Both sides got some lousy leaders, for the North they were mostly in the East (Burnsides, Pope, McDowell, McClellan). But for the Confederacy, there was an equally long list of bad senior officers: Johnson, Johnston, Hardee, Bureaugard, Bragg, Polk, C. E. Smith, Hood--all of them did poorly as Army or Corps commanders. And for those who would still insist the South had more great leaders, look at it this way: when the South lost Jackson, they had no-one to replace him with (and probably failed to exploit the success of Day 1 at Gettysburg because they had Ewell instead of Jackson). When the Union lost Reynolds or Sedgwick, they simply slotted in Hancock or Meade.
--Artillery: the Union had more of it, better guns, better organization, and better leadership of their artillery. Artillery (for the Union) was the deciding factor at Shiloh, Stone's River and the 3rd Day at Gettysburg. You can't find a single major engagement where Confederate artillery was a positive factor or even contributed to a draw for the South.
--Markmanship: the North had a huge advantage here. First, the North organized specific units of marksman (Berdan's Sharpshooters are just one example). Second, most of the Southern boys showed up with smoothbore muskets from home some of which had been handed down from their father or grandfather. The Northern boys were issued rifled muskets from the armory. Field tests done by solders at that time on the same range showed that rifled muskets had better distance and better accuracy than smoothbore, especially once you got beyond 100 yards.
--Navy: the South's was small, the North's was powerful. They successfully blockaded every Southern port and captured most, took the Mississippi.
--Supplies: the North, besides having industry, had more agriculture. The South just outproduced them in tobacco and cotton (and you can't eat either). The North produced more corn, wheat, fruit, cattle and horses.
--Supply lines: once the Mississippi fell, the South's supply lines were a mess. They were never good anyway because of the poor road system and limited railroads.
--Logistics: as bad as the Union's quartermaster corp was (corruption was one factor), the Confederacy's was a disaster. Confederate troops always lacked for every single element--food, shoes, rifles, cartridges, horses, uniforms--you name it.
--Superior leadership in the West. Except for the battle of Chickamauga, the South failed to win a single major engagement in the West. It's one of the most stunning examples of incompetence and military failure in any war lasting more than 2 years. Meanwhile, leaders like Grant, Sherman, Thomas, Sheridan, and Wallace were just kicking serious butt over and over and over in the western theater.
--in the middle of the war, with both sides badly bloodied, the North added 200,000 fresh, highly motivated reinforcements (US Colored Infantry).
--Leadership: the Commander in Chief for the US was Abraham Lincoln who all historians regard as no worse than one of our five best presidents. The CSA had Jefferson Davis.
--coherent military strategy (the anaconda plan) while the south had none. The decision to go into Maryland (leading to Antietam) was to get additional recruits--this was a failure. The decision to go into Pennsylvania was because Lee didn't want to give up any troops to Vicksburg and hoped to gain supplies (which led to Gettysburg). Strategy in the west was even more incoherent for the South. Shiloh was an attempt to prevent the armies of Grant and Rosecrans from uniting (but by attacking Rosecrans came to Grant's aid). Almost every major offensive operation by the Confederacy ended up as a disaster--it failed in it's objective and produced horrendous casualties that wrecked the South's warfighting ability.
Here are the advantages the South had:
--Superior cavalry. The Union cavalry was poorly led, poorly organized. This was exacerbated by the reality that the Confederacy produced some first rate Cavalry leaders: Turner Ashby, Nathan Bedford Forrest and JEB Stuart.
--Usually they knew the territory better. This was a combination of skilled use of mapmakers (especially by Jackson and then Lee) as well as often fighting on familiar ground (for instance Jackson knew the field of 2nd Manassas, Pope from the western theater did not).
--In the East, the combination of Lee and Jackson versus some inadequate leaders led to a series of successes that produced a very confident and cohesive Army of Northern Virginia. Note: this was not much of an advantage--it led to their downfall in other engagements when people like Henry Heth got too cocky and started fights they though would be easy to finish.
The argument that the Southerners finished at the top of West Point is just plain wrong. Lee was superb. But Pickett was notorious for finishing at the bottom of his class. Grant finished low. But Reynolds and McClellan finished high.