HTML is a bad choice - I want to be able to reorganize my site without have a million dead links. Even if I know what the correct organization is today, requirements will change and so in the future something will be wrong.

With rST I can link to a section and move that section to a different document and the links all still work (or if they don't I get an error for each and so I know where to look). With markdown and html I link to a specific document and since each is a document generator there is no warning if I typo the page name (there are a number of tools to look for dead links in html). With markdown I cannot link into a section of the page, only the page itself (some extensions to markdown allow this)