One big thing I still miss with org-mode are explicit section endings. Just as with markdown you only have headings, the end of a section is implicit. This often leads to text getting swallowed up by the last chapter and makes any kind of restructuring fragile. HTML's <section> makes things much easier.

Having explicit header levels (similar to HTML's <h[0-6]>) is another annoyance, as that makes inclusion of one org document into another problematic and requires restructuring (somewhat workaroundable with "#+begin_src org").