Phillip Leigh wrote a provocative "what if" essay as a chapter of one of his books about this very conundrum or set of conundrums. The thesis has been assailed under many of the points already raised in this thread.
Allow me to parse a few "what might have been" issues to clarify:
1. Repeating rifles were privately purchased from private arms manufacturers. So the tube-magazine lever-action Henry was expensive, and fired a .44 cal. rimfire cartridge that matched no other arm. The lever-action rifle and carbine of Christian Spencer also had a proprietary cartridge, and as noted up post, as many as could be made were made and issued out. As for the expenditure of ammunition, there is the well-known tale of the 21st OH at Tullahoma and Chickamauga: Armed with five-shot Colt revolver rifles, they inflicted enormous casualties on rebel forces until they ran out of ammunition.
2. The breech loader vs. muzzle loader. Ripley's hide-bound and frankly unpleasant personality that proved irksome to so many, including Lincoln somewhat obscures a problem: insufficient arms, insufficient production base/ factories, a whole bunch of obsolete .69 cal. smooth bore muskets, and since his stewardship since 1855 of the Model 1855 .58 cal. muzzle loading rifled arms, the issued service rifle. For a time it was deemed cheaper and expedient to simply rifle the .69 cal. muskets, acquire enormous numbers of arms from Europe--which was perhaps simply necessary not only to supply Federal forces, but to deny stands of arms from the rebel purchasing agents!--and ramp up production of .58 muzzle loaders, which was done. Ripley's defenders point out that the Federal cavalry was wholly equipped with breech-loading carbines, which was itself a prodigious logistical feat. Some of these breech loaders used linen or paper cartridges ("capping breech loaders), others used unique proprietary cartridges of metal or gutta percha.
RESEARCH QUESTION: Could more have been done to provide infantry with breech loaders? Many units, such as some from Connecticut and other states, the Berdan sharpshooters, etc. acquired Sharp's capping breech loaders. The very first breech-loading percussion arm in the world, the Hall carbine, had once been turned out by Harpers Ferry, which had been destroyed early in the rebellion, so no machinery and tooling was left, presumably. In many ways an inadequate and at times even dangerous arm, the Hall was long-in-the-tooth, and those rifles that were refurbished by ruthless war profiteers and foisted on hapless units are the stuff of legend. Still... The derivative Norwegian Kammerlader was being used in that Scandinavian nation... The Prussian nädelgewehr or Dreyse needle gun was a rather homely and inefficient design, but it allowed Prussia an edge in the wars fought in Central Europe and Northern Europe at roughly the same time as the U.S. Civil War... Could the U.S. have produced a pattern of a capping breech loader in greater quantity during the Civil War?
3. The muzzle loading rifle cartidge was typically two pieces of paper, one encapsulating the powder charge, and the other encapsulating the powder envelope and the bullet. The other type, the Enfield-Pritchett favored by the CSA after much disatisfaction with other patterns, is made of three pieces of paper. In either case, the cartridge is torn open, the powder charge introduced into the barrel, and then the bullet is removed from the paper, or, in the latter case, simply introduced into the barrel and the bulk of the empty cartridge snapped/torn off and disposed of. Revolvers used a self-consuming combustible paper cartridge. There were private ammunition manufactories that produced paper combustible cartridges for handguns, that also produced combustible cartridges for rifle muskets.
RESEARCH QUESTION: Could the U.S. have done more to provide much simpler-to-use and less fumble prone combustible cartridges for the available muzzle-loading rifled arms? Imagine being able to simply introduce the cartridge "right side up" into the muzzle, ram it down, and shoot versus the motions and fine motor skills required to manipulate the paper cartridge. Some units privately purchased "rocket paper" or combustible cartridges and found them reasonably easy to use, and it did increase their rate of fire somewhat.
4. RESEARCH QUESTION: Might more have been done to actually train soldiers in marksmanship and the proper use of the sights on their arms than was done?
Those above issues strike me in order as the fundamental issues and semantics affecting the firearm technology of the era?