Editing ascii tables with no editor support is painful.
There's also some org functionality in vim plugins, though I've never used them, so I don't know how much they cover.
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 :)
If popularity alone were sufficient for technological choices, we wouldn't even be having this discussion (and we'd all be using Windows). I try to choose my tools according to how well they work for me. Markdown, in my opinion, is a poor choice compared to org, but I can use it to collaborate with others, no problem.
As for the transition from light markup to TeX, that's pretty much the point of the OP, isn't it? Maybe the break point is different for everybody. For me, LaTeX imposes no extra cognitive load, but then again, I've been using it extensively for many years. If I'm need for something lighter, it'll be org (but really, org usually wins for me because of how well it does all the other stuff, not just the markup part).