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The Kindle is using MOBI because Amazon owns the format. The reason that the iLiad and Cybook are using MOBI is that there are no alternatives. No other vendor of DRMed e-books yet has a Linux Reader, and the only other announced Reader is Adobe Digital Editions which is "coming soon" for Linux.
In defense of MOBI, I would say that it is primarily a format for displaying e-books - rather than a format for laying out and archiving e-books. Even in this role it has limitations. Its real test will be whether it can adapt to displaying epub e-books.
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