I've been trying iBook and Amazon Kindle applications on my iPad and they are really good, but for sure I use more the Kindle application for reading my ebooks because I buy them for my Kindle DX and it syncs with all my other Kindle applications at my Mac, Android, iOS and PC, but Apple done a great job with iBooks on the GUI.
If you want to feel like reading a book at the iPad on a very great way, more human-interface and elegant you should choose for the iBooks and their ePubs, but if you want to read your ebooks on a lot of different devices, the best application is the Amazon Kindle one for sure, that you can sync all your books in many devices
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