Engineering was probably the most modern branch of the US military, it (along with the artillery) attracted the best officers, and Regular Officer training was largely based on engineering (which had quite a profound effect on the way the war was fought).
However, the Forts weren't mutually supporting. In fact they were generally sited far enough apart that smaller forts and the like had to be put inbetween them to stop the Rebs simply going through the lines. Hardly surprising when you've a vast perimeter (37 miles) to defend and only 1/3rd the guns the Russians had to defend Sebastopol (which had a firepower density 10-20 times that of the Washington defences). There were 6 major fortifications at Sebastopol on a frontage of 2 miles, with over 1,000 guns, on the same frontage around Ft Stevens I count about 50 (depending on whether you count light 6 pdrs and the like) and about 10 Mortars (depending on whether you count Coehorns)
As to general troop quality, the brutal form of natural selection practiced by both armies did create decent marching armies, but never really addressed some of the real shortcomings that led to some serious tactical deficencies, which also helped shape the battlespace in a downwards (i.e. dig in) direction.
However, by 1864, both armies are passed their peek of efficiency (which probably occured mid 1863), as the meatgrinder, and the expiration of enlistments meant that most of the armies were new enlistees.
As far as troop quality I will take combat veterans against green troops every time unless the technological difference is vast or the veteran troops got their experience by fighting armies much weaker then themselves. Neither is true of both armies of the Civil War which used basically the same technology as the European ones and had a considerable number of veteran troops even in 1864. The European troops would have been massacred by American ones in equal numbers after late 1862. Most American troops by that period would not panic easily, would know which positions to pick to hold their ground etc. Most European troops would have been green and would panic comparatively easy, would make tactical errors in picking positions to hold etc. just like the American ones did earlier. Even the officers, not talking enlisted, would tend to make more errors. It is one thing to make decisions on paper or even an exercise then to make them in a real battle field where you can get killed, people are screaming in pain all around you and the troops sometimes panic. This is true of the Americans too but by late 1862 they are used to it and the Europeans are not.