Since the original comments thread is getting long and too varied, I figure it's time to branch off discussion.
I must say that when I first approached the subject, I agreed with the current use of namespaces, since I have done a fair amount of object-oriented programming it fit within that paradigm, but after I did some more research on the subject it became apparent that the current implementation is not using the namespace concept in a standard way, and that using a pure category solution would be better.
The current use of namespaces isn't truly "bad," as it is non-standard. Name spaces are generally used for separating different classes of articles, not so much on their content, but on their use. For instance, the discussion pages are actually in a different namespace, along with the help pages.
Any time that the content needs to be organized, it is done through categories, which allow for both a tree-based structure, or more complex charting of relationships (since it is possible to have multiple parent categories). As I pointed out, Wikipedia, the largest wiki in current existence, has less than 20 namespaces, and thousands of root categories. Each of those namespaces contain data that is of a completely different use (except for the several types of talk pages, but I think that is just namespaces can't be nested).
Even though I was the one that linked to this, I believe that that part of the article is poorly worded. (I may even edit it...) A similar and better analogy is that the namespaces are like the file cabinets themselves, or other storage devices.
As I said, the use of namespaces for root categories is not the intended purpose of them. That is not necessarily a bad thing. You may be taking advantage of certain properties of namespaces that are not available as categories, but it is a hack. It may be a clever hack (and I am often impressed by and use clever hacks), but hacks should rarely be part of a permanent solution unless there is not other option.
This is true, and it is used "properly." I would merely suggest that you extend this concept to the root. It doesn't make much organizational sense to not include them in the same manner.
Certainly it works the way that it is set up, and there is some weight to that, as it might be difficult to reorganize things now, but given the disadvantages listed by Borror0 and given that it is improper to use them as we do now, and that the category system should be able to be used to a better effect, unless it would simply be too costly to do, the articles should be switched to a purely category system. (I'm willing to assist with that effort)