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My calibre library is over 5,000 books and documents and I use both iBooks and the Kindle reading ap for iPad -- I'm constantly shifting between the two. Amazons free storage and ability to sync documents between devices is invaluable and Amazon will never support ePub in the foreseeable future. As others mentioned, storage is cheap and that whole library with both mobi and ePub is less than 7gb with metadata and covers all included. But, as good as the iPad 3 is for reading, my inexpensive Kindle e-ink gives my eyes a better longer read and syncs beautifully with me iPad -- so rather than delete one format over another, do consider keeping both major file types. Keep your options open.
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