To me, one big issue is that you cannot use markdown to present everything, for example, one cannot use it to produce something like <pre>`d`<pre>, I mean he cannot use ``d`` to do that, right? Also you cannot write

```

```markdown

## HEADER

```

```

to produce a fenced code block which contains a markdown source code for code block.

Also, different markdown editor use different markdown parser. So, same source code will be rendered differently in different editor.