I think basically the difference is that Joplin is mostly a Note taking app while Obsidian can do quite a bit more. For me one of the main features of Obsidian over Joplin was the Dataview plugin, but there is also a simple way to convert your note into presentation slides. Using Obsidian as a todo app is also a bit better than Joplin. Finally, the mobile app the Obsidian offers is more complete than the Joplin app. One annoyance I still have with Joplin app on iOS is that I cannot use it for multiple profiles. In Obsidian it was easy to use multiple vaults.
Having all said that, I still reverted back to Joplin. The way it handles attachments was indeed one of the reasons to do so. I'll still use Obsidian next to it just for some temporary vaults, so to circumvent the lack of multiple profiles in the iOS app.
BTW I found the way to move an Obsidian vault to Joplin. Obsidian has a community plugin called Markdown Export. It will export folders in the fault to Github compatible markdown. This can then be imported by Joplin, including the attachments.