Personally, I would like to see a markdown spec that eliminates parsing ambiguity by restricting the "edge-case" features that HTML is really much better at describing in a standard and structured way.
I think we could pick one way to handle emphasis, lists, and code blocks that covers a specific and predictable 80%.
Anything that becomes hard to describe without including additional notation to the grammar is probably best suited to be left as HTML, as was the intention behind markdown to begin with.