Collaboration
Tragically, even if one finds an effective note taking method and set of tools, it only takes inviting one person to your space to render your knowledge base utterly useless and unnavigable (both to YOU and to THEM). A guest is not you, and therefore will usually struggle to navigate the space you've created for yourself. Worse still, the chances of them following your methods and habits to the same degree that you have is practically nil, and becomes increasingly impossible for every person that gets added to the space.
Here, the greatest unsolved problem of note taking rears its head: How do you grow a knowledge base where hundreds of people of contribute over the course of many decades into something that's at all, useful? It brings to mind Wikipedia, the greatest and largest of the accessible and browseable fountains of knowledge. Even there, hidden behind the final delivered pages, are thousands and thousands of discussions and arguments over what is essentially, curation.
As the volume of input increases, so does the importance of curation. In the context of a single project or department it's not too much of a concern, but once you have disparate groups of people contributing to different initiatives all under the same umbrella, it quickly becomes impossible to make sense of it all as a whole. The quality of note taking and organizing staggers severely. In this situation, massive amounts of work is created and lost forever shortly thereafter, repeated frequently, and everyone navigates whatever small set of alleyways they've been privy to and nothing else.