Not really a wish list item, but more of a suggestion since I see the author is quite interested in using an easy plaintext markup language for content formatting using markdown etc.
Have you had a look at Deplate? deplate.sourceforge.net/
It’s a VERY powerful markup language written in Ruby. I’ve been using it for the past year or two for virtually every document I make and I’m able to do a lot more in it than in MMD.
Would be great to find support for it in Scrivener similar to MMD