The thing you should understand about the U.S. Army in 1861 is that it was puny, to a degree beyond laughable. A nation of 30 million people had a standing army of 16,000 men, with no unit larger than a regiment. About half the Regular Army at any one time was garrisoned on the frontier in small posts, averaging about 200 men each.

There was no true general staff; what top staff officers there were usually held permanent field officer ranks, with a brigadier general rank being held by Brevet (Joseph E. Johnston was a lieutenant colonel, but held a brevet Brigadier General rank as Quartermaster-General of the U.S. Army). There just weren't a lot of generals to go around when the war broke out; certainly not enough to staff an army that would eventually surpass 600,000 men. In fact, one of the nine Department commanders in the 1860 US Army (most of whom held their ranks again by brevet) actually surrendered his whole department to the Confederacy and resigned from the Army at the secession of Texas to fight for the Confederates. Like most other generals in the US Army at the time, the man was ancient.

By comparison, Lee had served with great distinction and energy under Scott himself (Scott's main rival, Jefferson Davis, who had taken up Zachary Taylor's mantle in the pedantic bureaucratic feud, had already left for the Confederacy, as did his main protege, Albert Sidney Johnston; both Johnston and Lee had commanded the two elite cavalry regiments of the prewar army), and was comparatively young; the department commanders of the 1850s, and Scott himself, were generally veterans of the War of 1812, fifty years prior.