A couple of quick things, as I am sure someone will give a better, more in depth answer.

Lincoln did not have constitutional authority to end slavery. He knew this. Slaves were legally considered property and the federal government did not have the authority to simply take away that property.

One of the big issues was that as the country expanded the north was fighting to make those new states free states. Many in the south felt that this would lead to an end of slavery and a destruction of their economy. The fear that slavery would end is a major reason why the south seceded. You can look at their own documents, the CSA constitution, the different states official declarations of secession etc. to see that maintaining slavery was the major reason they wanted out of the union.

Lincoln did free the slaves in the south as they were then considered captured property, once the war was going, he did not free the slaves in the north because he had no authority to do so.

As for the reason, Lincoln did believe the southern states had a constitutional right to secede from the union.

Not trying to stifle any further contributions on this topic, but a similar question was asked not too long ago. You might find some relevant information there.

In order to answer this, we should probably look at Lincoln from three perspectives: his personal opinions on the issue of slavery from before the war, his reasons for opposing secession militarily, and the shifts in Lincoln's views, and the nation's war aims, which occurred after 1862.

Lincoln was, by heritage and experience, personally opposed to slavery. Though born in Kentucky, a slave state, he spent most of his childhood and almost his entire adult life in Indiana and Illinois, both free states. His parents were abolitionists, as were many of his neighbors. But he had more than local public opinion to guide him in this regard. As a young man, he helped take a riverboat down the Mississippi to New Orleans. While there, he witnessed black people in literal chains for the first time, and was appalled by the experience. He remained thereafter staunchly abolitionist in his personal views. Publicly, he took a slightly different tack. He was very clear, notably in the Lincoln-Douglas Debates of 1858, that slavery was a moral, political, and social evil. He made explicit his belief that blacks were human beings entitled to protection under the law. But he was not a radical. He publicly stated that he did not wish to make voters or jurors of blacks, or to raise them to full equality with whites; it is unclear whether he truly believed this, or if it was a sop to conservative Illinois voters. Further, recognizing that the nation was not yet ready for full abolitionism, he advocated a very traditional doctrine: the idea of restricting the spread of slavery until it finally collapsed under its own weight. Until at least 1862, he held to this goal (which, combined with his statements against slavery, was quite enough to earn him the scorn and hatred of the South).

Lincoln was elected on this platform, and it was this platform which inspired the southern states to rise in rebellion. As a last attempt at compromise, he formally pledged not to interfere with slavery in the states in which it was already in existence. This did not satisfy the future Confederates. Clearly, then, Lincoln did not plunge the country into war for the purpose of abolitionism. This claim was made against him, but it is not true. In fact, when John Fremont, then commanding general in the west, attempted something of the sort, Lincoln sacked him and reversed the order. Put plainly, he went to war for the immediate purpose of defending Federal forts and other property, and for the general purpose of preserving the inviolability of the Union.

Finally, we come to the shifting nature of the war's goals. From a war for preservation of the Union as it was, it gradually became clear to Lincoln that slavery was at the root of the issue. To strike at slavery was to both weaken the Confederacy economically and militarily, as well as to attack the reason for their secession. Quite a bit prior to the Emancipation Proclamation he had been contemplating something of the kind, but the fear of outraging the border states of Kentucky, New Jersey, Delaware, and Maryland constrained him. This is largely why the Proclamation, when issued, only applied to "states in rebellion," which, not coincidentally, contained the bulk of the nation's slaves. He still did not seek to fully raise blacks to equality, and contemplated the idea of sending them off to a colony, an idea that abolitionists received with scorn. But, yet again, we see Lincoln evolving, and by the end of the war it seems he had abandoned the scheme for colonization and come to increasingly favor full equality. Sadly, his death shortly after the Union victory means that we will never know quite what he would have done.

McPherson, James. Battle Cry of Freedom

Allen C. Guelzo. Lincoln and Douglas: The Debates that Defined America

Lincoln opposed slavery, but did not think that he (if elected president) had the power (constitutionally) to abolish it. (His election platform was to prevent its spread into new territiories - which he did think he had the constitutional authority to implement).

Both wartime expediency and wartime opportunity led Lincoln to issue the Emancipation Proclamation. He thought it would be useful. He also thought that using his war powers he could emancipate the slaves constitutionally (only in the rebellious states, not in the Union (border) states where slavery was legal).

Lincoln gave the 'reason' for fighting the Civil War, and expressed his views on slavery in his Gettysburg Address:

"Four score and seven years ago our fathers brought forth on this continent, a new nation, conceived in Liberty, and dedicated to the proposition that all men are created equal.

Now we are engaged in a great civil war, testing whether that nation, or any nation so conceived and so dedicated, can long endure."

Source: http://www.abrahamlincolnonline.org/lincoln/speeches/gettysburg.htm

In this great speech, that genius Abraham Lincoln managed to cover, in a few short words, both reasons for fighting the civil war: A democratic nation, 'conceived in liberty" cannot 'long endure' if the minority which is outvoted by the majority can just say, "Well, we didn't like that vote. We secede."

Democracy only works if a majority on a constitutional issue is binding. If it is not, democracy will not 'long endure' and anarchy, or some other form of government will replace it.

The United States was "dedicated to the proposition that all men are created equal". Slavery is a denial of that proposition. Lincoln ran on a platform to ban the further spread of slavery into the territories. He didn't think (if elected) that he had the constitutional authority to ban slavery in states where it already existed, but he clearly thought it was incompatible with the essential tenets of the 'New Nation'.

It was, of course his election, bringing with it the promise of banning the spread of slavery, which caused the secession, threatening the concept of Democratic government.

Lincoln, quite eloquently expressed that the Union was fighting for two reasons, to oppose slavery where possible, and to preserve Constitutional Democracy as a form of government.

The war made the abolition of slavery possible (constitutionally) in the rebellious states (at least according to Lincoln's interpretation) and he took the opportunity and acted with the Emancipation declaration.