Just a few of the weaknesses:
By 1860 the militia system, except for a few uniformed social clubs masquerading as militia, had largely fallen apart. Consequently there were few officers and NCOs who had any significant degree of military experience, assuming that one considered militia service as real military experience. The Militia Acts of 1792 and 1795, which required every man subject to militia service - which was every physically and mentally fit white male between 18 and 45 - to purchase a musket or rifle suitable for military service, had been ignored by both the national and state governments for years.
Just because a man was a social leader in his community, resulting in his election as an officer, didn't mean he had the skill set to lead men in combat. And, the governors used officer appointments as political patronage, which was a truly ineffective way of selecting competent officers. In this respect the U.S. Colored Troops were generally better officered than white units. Their officers generally had to have been experienced NCOs, had to pass an examination on military subjects, and had to pass a selection board composed of serving officers.
The national war reserve stocks of military shoulder arms - those still held by the Federals and those seized by the Confederates - at the beginning of the war were largely transformed smoothbore percussion or flintlock weapons. The weapons issued the states under the Militia Act of 1808 had largely been wasted through the incompetence of state officials and the few remaining weapons in state hands were in poor repair.
The new "soldiers" didn't know how to shoot military weapons at militarily useful distances and there was almost no one available who knew enough to teach them.
The Federal logistical system was incapable of supplying adequate quantities of almost everything military until late-1862, and the Confederate logistical system never was.
Helmuth von Moltke's purported observation that the American combatants were nothing but two armed-mobs from which very little of military utility could be learned was essentially correct.
Regards,
Don Dixon