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No, they aren't the same. The Mobi version is written in Java, the Gen3 version isn't.
The Gen3 version of the Mobi reader is considerably better than the iLiad version. It has much more flexible page layout options; it has a librarian; it allows you to view the book using whatever fonts you wish; it allows the customisation of the navigation menu; it lets you view the cover image - the iLiad permits none of these things.
They may well be the "same" in terms of the version of MobiPocket files that they support, but the Gen3 is a much more fully-features reader.
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