The biggest hurdle was price. Lever actions-like Henrys, Sharps, or Spencer carbines, and a dozen other makes and models of varying designs and calibers-cost more money than muzzle-loading rifles. Imagine trying to outfit an army of 60,000 infantry with an expensive and complicated weapon. Another issue was use of cartridges. You mention the Gatling, which did function, sort of. Using the powder they had available, and especially for the Confederacy, and severe shortage of copper, meant it was very difficult to produce intricate rifle parts and ammunition on a large scale. Added to this, is that many of these weapons performed well, but required maintenance that far superseded the relatively low-maintenance muzzle-loaders. A muzzle-loader's ammunition can be made with a lead mold, crucible, loose powder, and paper tubes. Individual cartridges had to made in a factory-and made well to function properly. What happens when you run out of the very specific caliber pinfire weapon you're carrying? You likely do not have access to exactly what you need, whether it be ammo or parts.

Unlike the modern US military, there was no single weapon model used by the Union or Confederacy, which is why some units bought their own (and early in the war brought their own weapons from home). Toward the later year of the war, some Union soldiers purchased their own Henry repeaters, and were able to vastly outgun their CSA counterparts. Point being, by the end of the war, both sides were recognizing the usefulness of repeaters, but only the Union was able to employ them in any sizable numbers. The war simply had too many men to arm, with too many variations in powder, calibers, manufacturing, metallurgy, and money issues to effectively outfit hundreds of thousands of soldiers with repeating weapons. To further illustrate the difficulty, even the troopers through the late 1800s out west were not often armed with repeaters.