Keep in mind that Slashdot lost 90% of its regulars due to poor decisions about layout change and an overly-heavy active comment section. On the other hand, the BBC and Guardian websites have picked up webby awards almost every year since the awards started.
The difference? The former became more cluttered and less responsive, the latter two (for all I detest some of the changes) are less cluttered and more responsive. That is key to a good UI.
Ultimately, though, any such site has data placed into a template, the templated data then placed into a bigger template. I see no reason why the templates should be fixed. They obviously aren't on Weirdpress.
However, that is only presentation. People need to be able to connect ideas. There is a way to do that - RDFa tags, DublinCore descriptions and SPARQL. You could subsume the tag system into that. What tag is primary would depend on where you approach the data from.