I’ll admit that putting Palpatine in Lincoln’s place was a really weird feeling at first, but I think it serves ROTS well in the way that it makes the Jedi’s suspicions against Palpatine feel completely ludicrous.
That comparison is already there, and the Separatists are already called the Confederacy. There are a lot of intentional historical parallels with the Civil War, with Julius Caesar and with Hitler. Lincoln did use emergency powers to raise an army really quickly and silence opponents during a secession crisis.
Making the Clone Wars about slavery just makes it more explicit, that’s all I was saying.