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There is a Kindle Web App now. Pretty nice. If you definitely like Kindle, you'll want both the App and the Web App. Going forward, the Kindle App will likely be the thing you use to keep a repository of Kindle books you already bought. The Web App allows you to store some of your books on the iPad, but you'll have completely free in-app access to the Kindle store and everything, while you're connected. A pretty keen thing Kindle did, recently. Allows them to stay out of the App Store marketplace, while still providing an app for the device.
 
So... to clarify:

Kindle does more.
Kindle has a better interface.
Kindle syncs better (i.e., at all).
Kindle has more book and author products.
Kindle book purchases cost significantly less.

iBooks is prettier.

/facepalm @ the fanbois
 
I agree the kindle app is faster, but I don't think that the Ibook app runs slow on the newer ipads. It runs much faster on mine than my friends. I'm just resistant to change I guess.

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The main thing I dislike about the Kindle app that the iBooks app can do is organize into categories. I have books organized mostly by classes or subject.

This is something that I have not seen the Kindle app being able to do.
 
I'd love to use iBooks, but where I live there is no non-free content in the iBooks store, while on Kindle I can access the full content. Until Apple actually gets content here, iBooks is nothing more than a glorified PDF reader.
 
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