One of Lincoln's major flaws as a war time leader was that he was unable to identify really good military leadership. This was a problem at that time because the Army was not as professionalized as it is now. Nowadays, presidents do not typically have to pick generals because there is an Army system for doing this. But Lincoln had to pick his generals and he picked a number of bad ones and perhaps stuck with them too long. A major example of this is how long he stuck with George McClellan even as McClellan's lack of aggression frustrated him.
One of Lincoln's major strengths was the strength of his character and his determination. Lincoln absorbed many setbacks during the Civil War, some of which were (like McClellan being in command) at least partly his own fault. But Lincoln did not let the setbacks deter him. Instead, he learned from mistakes, accepted that they were partly his fault, and moved ahead. All the time, he kept the main goal of winning the war ahead of his own feelings or pride.
Because of his strengths, Lincoln was able to keep the North together politically long enough to defeat the South in the war.
I concur with Pohnpei with regards to Lincoln’s apparent indecisiveness in replacing McClellan. The president was willing to keep McClellan despite his obvious lack of aggression as a general. However, it should be noted that McClellan was popular among the troops and the president may have had a difficult time trying to find a replacement. At one point, Lincoln brought in Gen. John Pope but he was shortly forced to recall McClellan. Lincoln also delayed military conscription and only employed the draft after facing serious defeats.
Lincoln’s strength was based on his vision and courage. Despite a myriad of setbacks, the president refused to relinquish his push to protect the Union. He made mistakes and learned from them, for instance, the issue of conscription. Lincoln fought and defeated the Confederacy to achieve the goals he had set forth for the nation.