What were some of the deeply rooted historical differences (that caused the war) between those states that would make up the Union and those that make up the Confederacy?
I feel I can explain the differences pretty well, but I'm always interested in others opinions incase there's something I've never considered. Everyone has a completely different views when it comes to this war.
The deeply rooted historical differences lay in the disparate geography and climate of the two regions as well as the people who originally settled there.
The South has a long and warm growing season and deep fertile soils, a situation which lends itself to large scale agriculture. The people who originally settled there intended to profit economically and did so through the production of large scale "staple" crops such as tobacco, indigo, rice, and later cotton. Southern farmers were dependent upon European markets to purchase their products (cotton from the south was a principle supplier of English mills) and also as a place to purchase cheap manufactured goods.
The North has thin, rocky soils and a short growing season; but does have deep natural harbors and a number of navigable rivers which lend themselves to shipping and manufacturing. The people who settled that area were not there to profit economically but to establish in Winthrop's words, "A model of Christian charity." Manufacturing became the staple industry in the North as opposed to agriculture in the South. Southern purchase of European goods hurt northern manufacturing; Congress therefore passed a number of tariffs to protect Northern industry. The tariffs hurt southern farmers who had to pay higher prices and also saw their European markets limited and deeply resented the tariffs, the most famous of which was the 1828 "Tariff of Abominations." It was the tariff dispute, not slavery, which caused the initial dispute between North and South.
Slavery became an issue much later, but primarily because of the geographical differences. Before industrialization and mechanization, large scale agriculture in the south could not exist profitably without free labor supplied by slaves. The north had no need of slaves and, because of the somewhat religious nature of their founding, saw slavery as an evil. The slavery debate easily morphed itself from the tariff debate and deepened the rift between the two areas.
It was thus geographic and economic differences, not slavery itself, that caused the rift.
Of course, slavery played a part here. It's not (to me) so much that the North hated slavery and the South loved it. It's more that it was a symbol for the North of the idea that the South was made up of brutal and nasty people. At the same time, the South sort of clung to it in part because it was a symbol of their own "independence," their ability to be who they wanted to be. I see it in some ways as similar to a fight between parents and kids as to the length of a kid's hair or how low he wears his pants. It's not really about that. Instead, it's about who is in charge. I think that slavery was sort of like that for these two regions. It was just a symbol or a convenient thing to fight over when the real issue was about who was in charge. So one deeply rooted difference was a difference of opinion as to who should have power in the US.
I think that the difference in the cultures of the regions was an important difference as well. The South saw itself as the land of chivalry and gentility. It saw the North as money-grubbing and soulless. It was sort of as if the South saw itself as living the good old days before industrialization while the North saw itself as a modern place with modern values.
Overall, I think that the differences (culture, economics, slavery) just made the two sides feel they were distinct from one another and that they had nothing in common.