The Capture vs. Retrieval Problem
Any note-taking system (or perhaps any knowledge system, including project management applications) has to solve two problems: information capture and retrieval. If information is not easy to capture, people will not add information to the system. If information is difficult to retrieve, it's not helpful.
It's a common problem in software documentation. Developers have tried to solve the capture issue by auto-generating documentation. However, this fails to capture more abstract information that needs to be written in different forms so that it can be understood by other people.
Capture vs. retrieval also relates to how and when information is structured. One criticism of systems like Evernote is that you need to define the structure before capturing information. This violates galls Law: By trying to design the system upfront, you will inevitably create an overly complex system that does not work and requires refactoring.
Some systems subvert this by giving you an "inbox." The getting things done system is one; knowledge base software like Roam is another. Both give you a place to put data in an unstructured way. Roam attempts to make retrieving it easier by encouraging links and creating a self-referential graph. The Getting Things Done productivity system solves this by adding a third step, a processing and organization page. It makes capturing easier by removing organization from part of the process and making retrieval easier because you will have a system intentionally designed after collecting information.