Org mode is great, particularly if you're already in the Emacs ecosystem because it can do a lot of stuff. Calendars, executable code blocks, spreadsheets, time tracking, org-roam for more ad-hoc notes and searching, capture templates for ingesting data...

I like org mode's markup format a lot better than markdown's. It's a bit easier to do complicated things with escaping and stuff, and it supports syntax highlighting for different languages in code blocks, and LaTeX markup and stuff (which it can even display inline if you want).

As far as I am concerned the only reason to use markdown is that more people are familiar with it and there's better support for it on certain platforms. These are certainly good enough reasons to use markdown, but in my experience if you're in the position to use org-mode it's just so much better.