As @nkozyra says, understanding what all the links do is hard, however there are automated ways of converting common types of webpage layouts into structure data for native presentation.
For example, our startup (shameless plug) utilizes a computer vision technology to automatically extract structured data from articles, images, products, and videos, etc: http://diffbot.com/products/automatic/. These can then be used to present native-experience views.
I was actually just looking at your startup for an application I'm building. Nice to see you on HN! Do you have an email I can use to ask you about cross-promotional opportunities?
Actually, RapGenius is the realized, "worse is better" version of Xanadu. It takes the simple idea of annotated hypertext and runs with it, and doesn't bother with all this unusual things like panning, backlinks, excerpts, and so on. That's why RapGenius is successful, and Xanadu is still vaporware.
OTOH, I don't think this is even supposed to come out. It's rather a demonstration of some pretty interesting, advanced (and thus also failable) ideas. It reminds me a lot of Jef Raskin's "Humane Interface" ideas.
Hard, yes--but I disagree with the premise that you have to design for 40 years from now.
Unlike the Colosseum, web design can be changed. The NY Times e.g. has done a great job balancing their time-tested values with digital experimentation.
I agree with you, too. For instance, it'll be a little sad if we're still writing MediaWiki macro markup in 2040. On the other hand, it's also probably smart to be wary of trendy designs, and Flipboard-like grids of story panels are very "on-trend" right now.
For example, our startup (shameless plug) utilizes a computer vision technology to automatically extract structured data from articles, images, products, and videos, etc: http://diffbot.com/products/automatic/. These can then be used to present native-experience views.