Tried both for quite some time, Obsidian has better community plugin support, better sync (paid) and stores plain text files instead of using a DB. Most importantly the mobile app (at least for iOS) of Obsidian is 1:1 with the desktop app.
Switched from Joplin to Obsidian and haven't looked back. Both apps are great initiatives though!
Does it reflect notebooks/folder structure also in the filesystem? That's exactly what I need from a PKM tool: that not only the files but also the structure of the notebooks is reflected in the filesystem so I can have interoperability. This way I can decide to work with Obsidian, EagleFiler, Notebooks.app or DEVONthink while also having the possiblity of using the regular Finder to work with my files.
Switched from Joplin to Obsidian and haven't looked back. Both apps are great initiatives though!