When I tried it awhile ago, the Kindle app had a page turning experience that can only be described as maddening. Tap in the wrong spot, boom, page has turned. The iBooks app, for all its over-done skeuomorphism, makes interacting with the book pretty easy. Simple things like page edges make clear what will happen when you tap in a particular place. iBooks just feels really nice.
More than that, the Kindle app is just ugly. It has this janky animation when you jump to another section of the book that's painful to watch. It's a shame – the Kindle v3 hardware is a pretty badass product. The Kindle iPad app feels barebones, insipid and unpolished. Does a disservice to the brand.