I don't see anything non-functional on the linked site at all. It just uses fonts and colors that aren't currently en vogue among the elite web 2.0 cadres. There aren't any background gradients. The text is white on black (horrors!) and somewhat larger than is fashionable these days (though why that should be a usability problem I don't know). It doesn't artificially restrict the text column to half (or less) of the browser width.
The worst thing is that there isn't even a shred of usability evidence anywhere in the post. When the author says that Jakob's site is "unreadable", what he's really saying is that he doesn't want to read it because it doesn't conform to his norms of aesthetics. It's like Picasso refusing to study Da Vinci because clearly he didn't grok cubism.