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Most appearance diferences between ePUB and Mobi are actually differences in the reading software. For instance, the same font looks different in the Cybook firmwares 1.5 and 2.0, because one uses Mobipocket's and the other uses Adobe's engine.
In my opinion, ePUB is superior to Mobi because it's more versatile, it's easier to convert/modify, it's an open standard and everything that can be done in Mobi can be done in ePUB too. But in particular cases, for a given book, or for a given device, or for a given user, Mobi could be more convenient.
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