But Markdown as UI... is less than ideal. It's great for hackers, but there's already a GitHub for hackers, and it's called GitHub. No matter how much prose.io prettifies it, you still get those damn asterisks all over the place.
Personally, I write in TextEdit, Helvetica 12pt. That's not a universal answer, but it works for me. (Previously I used MacWrite Pro, ClarisWorks and Word 5.1 at different times, but the basic appearance was the same.) Anything that makes a bold word look like "* * this * *" breaks 20 years of habit, and I won't do it.
Markdown as backend storage, fine. But not as the primary editing interface.