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.
Same deal with preview-latex - you can include LaTeX directly in pandoc documents, but no editor I know of will do previews of it for you. I do think that is an awesome feature though.
Overall I think the audience for Markdown is people who don't want to get down in the weeds with, say, LaTeX and Emacs like you do. Thus, the feature set for Markdown-focused editors is still fairly simple. Pandoc is useful because it lets you add a layer of complexity on top of your Markdown as necessary (through templates) and get it into different formats easily. (The same can probably be said for other Markdown systems like MultiMarkdown but I like Pandoc) I have managed to set up my workflow to get Pandoc-flavored markdown into an apa6 LaTeX template without any significant issues, due to pandoc being fairly flexible, but it's not quite at WYSIWYG-style writing just yet.