I guess I am a markdown hater, but I don't like it. Markdown feels too much like hand writing your own html, when you have to put in tags, but like html it suffers from lack of layout control, which is why they invented CSS, but you don't get CSS control in markdown. If you start adding that, you end up with LaTex, and I don't know anyone who actually enjoyed writing serious documents in Latex. It was fun in the beginning, but it quickly became tiresome and I found myself not being very productive.

Doing layout is not easy. Programming layouts well requires real expertise, which is why most layout engines expose a gui and let you deal with larger text components graphically. Maybe someone else will come up with a usability innovation here, but I'm not aware of it, and markdown certainly doesn't have that capability.