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The UI of operating systems hasn't evolved in over 20 years. I actually think ebook readers are transient phenomena. They will be replaced by UMPCs with reflective display technology. The suitability of semantic formats has nothing to do with the limitations of ebook readers.
And as far as the evolution of the web is concerned, it is becoming more semantic, not less. PDF is not a standard for "desktop", whatever "desktop" may be. It is a standard for fixed size layouts, but as I've already explained above, fixed size layout is a remarkably unimportant thing, once you truly give up the legacy of paper in your mind.
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