Re-think your "container paradigm"! Use tagged organization!
Back in the beginning of computer era the "container paradigm" used to dominate the way data was organized. Everything had to be saved as a file and organized in folders and those folders in other folders and then logical drives and so on. That was just a digital copy of how the world was organized before computers were invented. We just transferred the data organization methods on paper into our digital devices.
Pretty early the idea of databases came out and storing and finding big amounts of records could be done using them more and more efficiently, but for the "classical" data the "container paradigm" was never rethought! Today we still organize our documents in files and folders, the same with our digital photos and music
People even do it with new digital data formats like e-mail and ask for folder support to be added to their instant messaging services!
On the other side, Google has shown with labels in GMail and Twitter with hashtags that actually the best way to organize digital data is tagging, which is actually putting all data in a huge database, referenced by any number of tags.
The greatest benefit of the "tagged organization paradigm" is that you can have a piece of information referenced by several tags in different contexts without having to provide several copies of it that are difficult to keep synchronized.
Having a tag hierarchy, you can even build sets and subsets of information pieces, e.g. you can search for anything regarding "#pets" or for more specific items, "#pets.dogs". Both will show you the items regarding dogs, but #pets collects also information about other pets.
The point is, you still have some hierarchical organization like folders, but you only structure the references, not the content storage.
PLEASE add easy to use tagging possibility (like Evernote) and hierarchical tag organization to make OneNote the number one note taking and organizing tool.
That sounds too visionary for a lot of us, even far away from our needs and reachs. I must agree with you about the tag utility in Twitter or even Gmail, but notheless, using containers as the main hierarchy provider isn't wrongly focused. It is the way of storing everything in our lives, computers, history and probably in our minds too, the tag thing may add some richness to the stored information but I would never trust a system based on tags only.
Even with the containers and tags available, both of us can benefict from both systems, without the need of prioricing none of them.
I've never seen anyone organizing their belongings on a tag based system, at least not at domestic environments. Even as a programmer, i rarely use tags instead of containers.