Good points. An intentional stance that has note changed since 2008? There are four factors at play here.
1. Information Structure and Organization. gmail is an excellent example showing that "labels" and "folders" are one and the same. In fact, technically, any filesystem is simply a set of labels (tags) in a directory. The only difference is that tags allow multiple membership, which is a more flexible structure than a directory. I'd argue that EN users have a higher requirement for organizing active information than an email app, which is ultimately about Inbox Zero and an archive. This is the actual nature of the technical problem at the root of everyone's frustration.
2. User Stories / Usage Cases. Some people think in terms of folders. Some think in terms of tags. Some prefer search. Some problems (archival) favor folders and hierarchy. Some problems (research) favor jumping to a tag. Some (quick answers) favor a search. Take a simple example from Spotify, who has essentially solved this problem:
Playlist: My Deep House Playlist - a list of songs I MUST have together in a specific order (they can also be in other playlists)
Hierarchical Playlists: Electronic > House > Deep House; Electronic > DownTempo; Electronic > Dubstep; etc.
Tag: Artist names, albums, genres are all forms of tags: Metalcore, punk, Prince, JustinBieber,
Search: "Free bir..."
3. User Perception. The fact that this is an ongoing debate 10 years later, means customer expectations are NOT being met. Perhaps Evernote Team don't understand what the users are asking for. Perhaps they do understand but are dismissive. Perhaps no one with formal training in ontologies and information structure is even looking at the problem, so EVERYONE is confused both Evernote and Customers. But regardless, the fact that users aren't free to organize thousands of notes in a way that works for them, and the company and the users are talking past each other for 10 years running? Obviously a communication problem. Poor @engberg left alone to defend the company's position without reinforcements.
4. Technical Deficit. Evernote has been running a technical Deficit since the beginning. I'm a champion, and supporter and really WANT them to succeed. And they've managed to keep advancing the product so many of us rely on. But the reality of over-stretched technical teams, is long stand-up meetings with long lists of unresolved bugs. And the lists keep getting longer. If the technical deficit is never addressed, often by biting the bullet and focusing on refactoring ancient code, the problems compound, it shows up in quality, and it shows up in subscription renewals, and those paying customers are the lifeblood of the company. All it takes is a freshly funded Y-Combinator team who are super smart and super motivated to solve the problem in a cleaner way. Then when Sequoia backs that team, it will be able to hire the best engineers who've been slaving away to maintain the EN code base for a decade, and the rest is a story told a thousand times in Silicon Valley.
So, hopefully, this one widely desired and poorly understood aspect of information organization can be resolved AND communicated sometime soon.