What were the three most important factors in the Confederacy's defeat in the Civil War?

There were many factors which played a role in shaping the Confederacy's defeat in the Civil War, and I'd hesitate to winnow things down to just three. However, for the purposes of this answer, I'd focus upon the Union's clear advantages in production and population (advantages which proved overwhelming in the long run), the impact of long-term military strategy, and the South's continued reliance on slavery, which would serve to isolate it from potential allies such as Great Britain and (after the passage of the Emancipation Proclamation) would serve as a rallying cry among those opposed to slavery.
Of these three, I believe the most important was the sheer quantitative advantages the Union possessed. The Union had a much larger population (giving it a far greater ability to replenish losses, an advantage Grant would use to devastating effect) as well as manufacturing centers. They outnumbered and outproduced the Confederacy. Even in the field of agriculture, they tended to hold the advantage (given that so much of the Confederacy's agricultural production was tied up with cash crops). This meant that, in a long term conflict, the North would inevitably hold the upper hand.
In addition, it's worth noting that the South's reliance on slavery itself weighed against it. Its most natural ally against the North would have been Great Britain, but Britain had, by this point in time, taken up its opposition against slavery. This left the Confederacy isolated in terms of allies; and later on, the Emancipation Proclamation would give the Union Cause a second wind of sorts, turning the war effort into a cause against slavery. Of course, it should be noted, that this move was controversial in its time (especially for those who had conceived of the Civil War purely in terms of being a war for unification), but it was an important factor nonetheless.
Finally, it's worth discussing the competing large-scale military strategies which guided both sides. For the Confederacy, the Civil War was largely a defensive war, with most of the fighting occurring on Southern soil. This meant that, as the South was the main theater of the war, the fighting left the South far more ravaged than its northern opponent.
Meanwhile, the Union pursued a methodical approach, beginning with the blockade of Southern ports (which proceeded to greatly weaken the Southern economy) and continuing with the capture of the Mississippi River, which divided the Confederacy in half. This culminated with the advances of Sherman and Grant, which forced the South's surrender.