I've been living in Emacs + Auctex for a while now, so my questions about markdown/pandoc: I have grown very accustomed to regex (and normal) searches on my bibtex/reference database and easily plugging in citations in my document. Is there support for this (reftex) in any of the markdown editors? I don't know if I've seen a good solution to this.
The other thing is preview-latex which inline-png's all equations, section titles and images in the emacs buffer. This is very valuable to me to easily see a figure without needing to tab between windows. I don't think markdown would support something like this, as far as I'm aware.
I like the idea of complete separation of content and appearance/layout, but Latex has many customizations (psfrag for image text replacement, tikz, programming custom macros) that I would be somewhat lost without. For instance, I start all my outlines in org-mode, and love having quick html, or tex->pdf output, but for the real nitty-gritty content, I _need_ my straight latex code.