Don't limit yourself to Kindle or iBooks. Explore these forums for mentions of other readers. Checkout Bluefire Reader, Kobo, uBooks, Ebook Reader, nook, Google Books, eReader, GoodREader, and MegaReader apps for iPad. Some have more options than others. If you use Calibre (mentioned above) some will connect to all your books in the Calibre library. In other words, you can download books over wifi.
Out of the ones mentioned I highly suggest trying MegaReader and BlueFire.
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