If it were up to me, I'd simply ask that markdown add support for h3 (other than hashes, e.g. Underline with hyphen and spaces) -- two levels of headings is all too frequently insufficient, inline links to images be rendered as image tags, inline links to videos etc. likewise become video tags, etc., the way other inline links become anchor links, and some form of table support be standardized.
Aside from that (and implementation bugs) I've been very happy with markdown.
Using Pandoc, what my habit has become is have the first line at the top of the file be title metadata:
% Title Goes Here
then make subsequent headings go ahead and start at h1 (rather than h2):
Some h1
=======
This puts an `<h1 class="title">Title</h1>` at the top, with regular unadorned h1's further down the page. So, if you like, you can style the title h1 differently from the other h1's.
It breaks the soft rule of having only one h1 on a page, but otoh looks good, and doesn't require me to go to h4 or h5 very often, so I can live with it. :)
Aside from that (and implementation bugs) I've been very happy with markdown.