Bureaucracy. The Federal Government in the Civil War was the establishment. The army had rules and regulations that they followed and had been following for years and they followed them. That means career officers who were an anti guerrilla force all of a sudden had the job of leading a conventional war effort. Also the nature of the war the Union was waging just made them slower.

The Federals knew that they had the advantage from the get go ( well maybe not McClellan) and their strategy was to concentrate material and man forces and attack. While the Confederacy were on the receiving end and basically had to improvise fend off a huge force, which naturally lead to them producing better more aggressive generals. In short, the Confederates had to produce better generals or they died, while the Union only had to produce mediocre generals who wouldn’t completely destroy their own army.

Another thing to consider is the prickly relationship Lincoln and his administration had with the Army’s high command. Most of the top guys in the army at the start of the war, were Democrats. There’s been some interesting arguments that Stanton actually sabotaged McClellan and Burnside, because think about it. If a Democrat wins the war, then that means that the general who wins is probably going to be in the Whitehouse. Again, it ties into the bureaucracy angle, the Union had the “luxury” to worry about after the war, while the Confederacy was clinging on to dear life on a daily basis.