The major difficulties that the Union Army had to overcome during the Civil War were the pressure of politicians to adopt an aggressive war strategy, and the lack of leadership at the beginning of the war and a shortage of manpower in the second year of the war.
Explanation:
The first problem that beset the Union Army during the  U.S. Civil War was the  pressure place by politicians to wage war aggressively against the Confederate States in order to put a short end to the war. The Commander-in-Chief of the U.S. Army of former Mexican-American War glory, General Winfield Scott, had proposed a mid to long term strategy that he called "Operation Anaconda" to win the war by blockading both land and sea commercial routes between the Confederate States and its trade customers abroad such as Britain and France, in an attempt to minimize the loss of human lives and destruction of property. However, this plan was considered too cowardly so it was ridiculed and rejected by the most influential politicians in the North who wished for an epic war and an exemplary punishment for the rebellious South.
To compound the problem, the best general and worth of General Scott's trust to conduct the war, General Robert E. Lee, refused the command of the Union Army as he felt more allegiance for his home state, Georgia, a state member of the Confederacy. Furthermore, the commanders appointed by president Lincoln were incompetent and defeated one after another by the brilliant generalship of Robert E. Lee. This lack of effective leadership would not be fixed until the battle of Gettysburg.
And last, but not least, the initial defeats of the Union Army at battles like Antietam, Bull Run, among others, had taken a great toll of casualties and desertions which threatened to severely reduce the number of soldiers that the Union could field against the Confederacy. Much to the chagrin of people in both sides of the conflict, president Lincoln ordered the creation of regiments made up of African-American volunteers whose combat worthiness was constantly challenged as they were trained. One of such regiments, the 54th Regiment Massachusetts Volunteer Infantry, would serve in the war with distinction and gallantry.
