Naturally, a format with more metadata loses metadata when converted to one with less (and the reverse, you may need to add metadata in when going up the chain), but unless your document is bound to a specific format (in which case, I'd pick RST for HTML and LaTeX for pdf), markdown gives you the content and pandoc lets you specify a template (and with pandoc, you can take the markdown and generate slides in HTML, PDF and create notes through the different outputs).