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.