Just as some examples: outline-centric without plugins (this allows functions like narrowing/hoisting to a particular part of the outline that you can't do in Obsidian), substantially better export/document authoring, org-babel (think Jupyter style notebooks or literate programming) integrated into the core concept, functionality integrated into the core system rather than siloed into plugins (org-agenda is essentially a combo of the dataview plugin and the todo plugin in Obsidian, but built to work together, and completely integrated with things like timekeeping/clocking for those who bill hourly, which is still missing from Obsidian). Plus some of the keyboard-centric stuff in org-mode is just really nice, down to little niceties like how you can manipulate dates and times without clicking around. Then there's all the benefits of emacs on top of that.
To some extent a lot of this derives from org's 22 year history. It's a very mature system, with loads of functionality.
One strength of Obsidian though is canvas mode. There aren't great emacs solutions like that at the moment.