I think Joplin will never be a great Zettelkasten tool, because of its basic structure which is build around folders and and sub-folders combined with tags which are not really part of a Zettelkasten
That said every persons applies Zettelkasten or similar methods in very different ways and I think Joplin could be much better in supporting them. As stated before Transclusion and a Graph View are nice features, but for me linking notes together is the main point. I am writing a meeting note and want to reference something from an earlier meeting or I learned something new and want to connect it with some old lectures notes etc. Learning and making sense is about building connections, links between notes.
You can argue that we have plugins for that already, but I think they are not user friendly enough. The backlink plugin does not automatically add backlinks to to the Markdown-Editor and while writing a note I am not always switching between Editor and Viewer pane. Its just difficult to keep track of the connections of a note. The quick links plugin is great. I still think its annoying that it uses @@ and not [[]] , but I got used to that. But its not dynamic. If I change the title of a note the link is not changed and if I click on a link I cannot open them side by side, I always have to go back. But most importantly their is no UI to link to headlines within a note (there is not autocomplete for headlines). In Joplin I write long notes with subheadings. For example I have a long note which deals with LaTeX basics, but when if reference it in another note I want to link to one subheading. In addition to that there is the problem of mobile app support for these features if I want to write a quick note and connect it to something else.
I think the essential features are already available but the implementation is not as easy/straightforward as it is needed for note-taking.
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