How could Lincoln have justified ending slavery as a war time measure in areas not under rebellion---or from loyal Unionist owners? A wartime emergency still requires a positive link. Ending slavery of loyal Unionists was not necessary for the war effort. Had there been a direct link or necessity, then perhaps he could have. But this was not the case.
I made the analogy below, with Ken, about police officers confiscating weapons. Such action is only legal or justified when a direct cause can be shown, and even then there will be critics. A police officer may confiscate property from a suspect in order to deal with a dangerous situation. That police officer could not justifiably confiscate property from everybody around simply because he wanted to, without an identifiable reason or link to public safety, etc.
As for why slavery was not abolished sooner, I would argue that it was abolished remarkably quickly. Considering the fact that only radicals and extreme abolitionists considered a constitutional amendment outlawing slavery in 1860 and 1861, the reality that Congress got its act together by 1865---in four years---to overturn a major American institution is really amazing.
Even the move against slavery adopted by many Republicans as a wartime necessity was slowed by fears of sending loyal slaveowners and the border states into the Confederacy. Forcibly ending an institution as ingrained in Southern and American culture as slavery was not something that was taken lightly. Many in Congress, particularly Democrats, strongly opposed even the Emancipation Proclamation. It is not a surprise that efforts to abolish slavery constitutionally would find obstacles.