I worked with the Wikipedia category system a few years ago, and you could see the problems with hierarchical tagging systems right in action back then. (Though it may have gotten better in the meantime) The system appeared simple: There were just two relations, "Article A is a member of category B" and "Category X is a subcategory of category Y". However, in practice, the community was using this system to represent…
I think the problem is allowing users to freely tag, then. There should be easily accessed guidelines about how each tag should be used, and people who are constantly moving them, correcting them, and updating usage guidelines.
We need the ability to implement governance systems on top of web 2.0+ style content systems. People should be able to vote for representatives (with any number of voting systems), create committees, submit changes to be voted on, etc. Instead we usually work based on hierarchical dictatorships or imagined consensus. People need organizational management tools baked into software, because organization of information depends on it. Instead of proposing a new committee to come up with the schema of everything, better tools that enable users to build committees.