One of the more crucial weaknesses of the Union army was its lack of experienced generals. Most of the military colleges were located in Confederate states. As a result, Lincoln found himself commanding generals who could not capitalize on the weaknesses of the Confederate army.
Another big disadvantage the North suffered was the fact that they were invading an unknown territory. Generals in the South knew the lay of the land, and they knew how to harass Union troops, whereas the generals of the North were not familiar with the area. Soldiers of the North also had to face an enemy that had very high morale because they were defending their homes. Finally, the objectives of the Union army, both political and military, were very broad and much more difficult to accomplish than those of the Confederates.
All the Confederate states had to do was survive until the end of the war, whereas the Union army had to invade, conquer and then subdue the enemy. They had to take the Mississippi River from the South in order to impede western supply lines. The North also had to cut off the South from international traders and stop the South's manufacture of war supplies. Finally, the North had to stop the Confederate army from invading northward to take pressure off of the North's early losses.