Well there are a few things to address here.

In regards to the Civil War, saying that the war would have been shorter if the Union was all armed with repeating rifles (or single shot breechloaders even) is hardly the same thing as saying it was feasible to arm them all as such. I wouldn't disagree that the increase in firepower such an upgrade would offer might have an incredible influence on the course of the war, but we are getting into counterfactuals, and that discussion is best left to /r/HistoryWhatIf. What I can say is that this would require the quick production of hundreds of thousands of rifles for distribution, the prospect of which I find to be dubious. The mixture of singleshot and repeating breechloaders being produced in actuality was a massive hodgepodge of types in numerous factories, big and small, but this wasn't enough to provide anything approaching uniformity for just the cavalry, and expanding such production for the entire Army would be far too daunting a prospect to pivot in in wartime. A stellar example of this comes to us later with the USSR, who had begun to switch over to the SVT semi-auto in 1941, but instead had to ramp up Mosin production due to the outbreak of war. Even ignoring cost, shutting down and retooling factories take time, and you don't have time to waste in those circumstances.

But as I said, this is all a little speculative. What we can say is that post Civil War, the US definitely lagged behind in firearms development. By the 1870s, we see bolt action designs start to show up in Europe, some of them even magazine fed repeating arms. The US instead adopted the 1873 "Trapdoor Rifle", which was an evolution of the Springfield Rifle, using the Allin design which had been used to convert earlier Springfield into breechloaders. The US played catch-up, introducing the Model 1892 "Krag", but the Krag was also a behind the times design, lacking the fast, clip loading ability that had started to become standard in Europe. When the US went head-to-head with Spain in 1898, the Spanish Mausers were better than the Krag in almost all respects, and the US knew what it wanted.

This brought about the M1903 Springfield, and you'd be hard pressed to find serious hate for the M1903 Springfield, which was essentially a modified Mauser design (patent violations were found in fact). It was overall a great rifle, and was considered very accurate. The Springfield was replaced by the M1 Garand in the '30s, and the Garand was plainly the most advanced standard issue rifle in any military at the time, being a semi-automatic rifle in a world of bolt-actions. I certainly won't get up here and say the Garand was the perfect rifle (although it has its vocal defenders), but after being kind of behind the times for quite some time, the US was now at the forefront for a little bit.

The Garand was followed by the M14, which while a pretty damned awesome battle rifle, the entire battle rifle concept (full sized cartridge) was dying out by then, replaced by the assault rifle concept (intermediate cartridge). It was a reliable enough weapon, accurate too, but heavy and bulky. Its life as the service arm for the US military was thus very short-lived, and the Armalites came on to replace them. The early M16s did have some significant issues in Vietnam, but they were really fixed up pretty quick the article stating "the M16 rifle that killed so many of the soldiers who carried it in Vietnam" is rather unfair, as I don't think there is any study which sticks a number on that. My focus is bolt-action rifles, so I really am not one to get into the nitty-gritty of the M16's teething pains. I would highly recommend "The Gun" by C.J. Chivers, which looks at the development of the AK-47 and the M-16 for a more in-depth look at this, although /u/Bernardito might show up and expound on this bit.

So anyways, that is about the sum of it. To TL;DR it for you, to question 1, it might have shortened it, but making and arming hundreds of thousands of repeating rifles is easier said than done.

And to question 2, the US decidedly lagged behind in the late 19th century, caught with the 1903, and led the pack into WWII when it came to rifle design, but afterwards, they remained attached to the Battle Rifle a little too long. And the hate that the M-16 gets in Vietnam is at least partially undeserved, although I'm not the guy to talk to about that. My interest in firearms is almost directly proportional to how much wood is used in their construction.

On the Civil War issue, I think the notion that a simple change in arms would have made a difference overlooks one of the core critiques of the Union Army: notoriously bad leadership. In the chain of Union commanding generals from McClellan to Pope to Burnside to Hooker to Meade, "competent" is the highest compliment you could ever pay any of them. Much has been written about poor strategic leadership at the head of the Union army until the appointment of Grant, and a change in weaponry wouldn't have solved that. As only one example, the absence of repeating rifles didn't figure in to Meade's decision not to pursue Lee after Gettysburg, despite being in possession of Lee's field notes and plan of retreat, and there's no reason to believe that having more repeating rifles would have made Meade more willing to press a hot pursuit and attempt to turn his victory into a decisive route. Napoleon almost certainly would not have made this mistake, and he had never even heard of a repeating rifle. Good tools don't improve a bad craftsman.

Someone's always going to look back on things and say, "you know what? We could have done that better."

It usually helps to look at a work critically. A favorite axe to grind for historians of WW2 is Belton Cooper's, "Death Traps" which gets incorrectly held up as a work of history rather than a simple memoir that got marketed as bitter truth and propelled into History Channel documentary hell.

Did I say memoir? That isn't entirely accurate either. He spends an entire chapter trying to claim there was a conspiracy to have the M4 named the, "Sherman" as a slight against the Southern US even though the naming tradition originated from the British needed to differentiate between domestic models and American imports. He also tried to blame General Patton for the continued use of the M4 Sherman even though he had nothing to do with the tank's development or requisition.

As far as weapons are concerned? Usually when someone looks back and says, "well, why didn't we use this?" they're usually ignoring- intentionally or otherwise- some critical factor. Just as an example, again, Belton Cooper couldn't wrap his head around why the M26 wasn't put into service earlier with no respect to the logistics it would entail to field the tank. Speaking to the civil war, I highly doubt the North had the economic means to properly retool, field, and supply semi-automatic and automatic weaponry.

Anecdotes make for good flavoring of history but don't carry much weight. A good stewed history requires a heavy portion of statistical meat and potatoes, if you catch my drift.

While not specifically regarding rifles, Max Hastings makes the case in his book Armageddon that the Americans in WWII, as well as the Allies in general, were greatly hampered by inferior weaponry. Most of the following is from pages 84-86 of the paperback edition.

The American bazooka and British PIAT were both extremely inferior to the German Panzerfaust and relatively ineffective against the German armor. Hastings states: "The Faust, vastly superior German counterpart of the American bazooka antitank rocket And British spring-loaded bomb-throwing PIAT, was the decisive weapon in enabling Hitler's armies to continue the war until May 1945, given the weakness of their artillery and almost complete absence of air support." He also quotes an Allied commander as noting: "Numerous cases have been reported where bazooka teams have succeeded in immobilizing tanks but since they are unable to destroy them they themselves have been killed by retaliating fire from the tank and the take retrieved by the enemy."

The M4 Sherman tank was also not on par with the equivalent German Tiger tanks. "If they fired at a German Tiger or even Panther their shell was likely to bounce off, unless it's struck it weak point below the gun mental or on the flank. Meanwhile if an enemy's shell hit a Sherman...it was likely not merely to stop but, to burn."

He also notes that the German MG42 had an "alarmingly faster rate of fire then it's Allied counterparts."

The Allied higher ups were almost certainly aware of these shortcomings as "[a] of deluge field reports descended on the US war department almost to the end of the war demanding more infantry forward units, a better tank gun, fewer duds shells, a better armor tank destroyer...a less clumsy submachine-gun than the Thompson, [and] an anti-tank gun more impressive than the feeble 57mm."

At least regarding the tanks the, US War Department recognize that the tanks and guns were weak against the enemy but concluded that the "quantitative advantage was so great that the qualitative issue did not matter." Basically the US had the industrial manpower and resources to replace any losses that they sustained and decided that it would be easier to do that then to redesign their tanks.