The main problem is that the entire idea is only half finished. Sure, the search engine side of things has been mastered by everyone and their dog, but there's another half of the equation that hasn't even been touched yet:
How do we actually add metadata to our files?
In some areas, the addition of metadata is pretty good. For example, when I rip a cd into mp3s with iTunes all the relevant song information is automatically downloaded from the internet and inserted without my having to do a thing. But what about images? Files received via e-mail? There are probably lots of other examples of files that could contain lots of additional relevant information, but don't.
The other issue lies in hiding the whole idea of searching behind a UI that users may actually use. I don't want to have to open an application window to access my commonly used searches. I'd like to have automatic folders, similar to the way the Recent Files folder/menu item works. It would be cool if they could be automatically created for me as well. I definitely don't have all the answers, but I'm pretty sure the entire experience could be a lot better. Who knows? Maybe this is where Microsoft is headed with WinFS.