Adding my +1 to a nested hierarchy. I actually discontinued my EverNote premium and switched to using OneNote because the organization was more intuitive to me than the tagging system of EverNote.
Since the ancient world we have been using hierarchical information structures to organize thought and information. That's long enough that there is probably an actual neurological adaptation to hierarchy as an information structure. To me, it seems like the concept of "tagging" relates more to virtual information structures than social or literary ones; the concept of a "tag" seems to have grown out of object-oriented information design vs. procedural information design and procedural has a few thousand years of human adaptation behind it while object-oriented design is relatively new (though admittedly it follows aspects/characteristics a heuristic model).
In more direct, less highbrow language; my brain organizes in hierarchy, not tags. I had to stop using EverNote to be more organized.
Seriously, the software should have two organizational modalities; a tagging structure for those who think in terms of aspects / descriptors and a hierarchical structure for those who think in bullets and lists. If you implement both, wider audience for the software.