I have two suggestions on the very top of my list:
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Zotero / BibTex integration for bibliographical references - this is a killer feature for students, academics, journalists, and many other people. Zettlr has that feature, but I prefer Joplin which is a much better note-taking platform overall. Since Zettlr is open source, maybe their implementation could be easily adapted for Joplin?
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An implementation of the Zettlekasten method allowing easy two-way linking between notes to connect ideas. This is increasingly becoming one of the most requested productivity features for note-taking software, and having this in Joplin would be amazing. (Zettlr also happens to have this feature, so maybe their open-source implementation could be easily adapted to Joplin.)
Apart from these two extremely useful features, I already find Joplin vastly superior to every other note taking software out there. It has quickly become a indispensable tool in my workflow, so let me take this opportunity to thank you for your fantastic work!