I find that you should use org only if you use Emacs. Vim plugins for Org are very limited, and this is even more true for other editors.
Judging a technology only for its technical merits is unproductive. Markdown has "won", it's everywhere and everyone can learn to use it. Those are damn powerful advantages.
Using Markdown, I gain the ability to read and write on a smartphone or tablet in my phone or tablet, which for some notes is extremely convenient. Many times being able to access my notes on philosophy from my phone during a bus commute allowed me to develop and write down a thought, which would have been a pain to do with other technologies. Of course I could have done the same with other options, but this ubiquitous convenience and effortlessness is great.
What I'd love to see is a way to transition easy-to-write-everywhere to more powerful type-setting easily when needed. May be combining Markdown and Latex? Or converting Markdown to Latex before publishing?
I'm sure this exists already; I just haven't needed it enough yet :)