My personal bias is being pro markdown. I do not know groff so below is based on some inferences on my part.
But I don't think markdown is suitable for man pages, which contain specific kinds of information structured in a prescribed way. Markdown doesn't and can't know about these.
As I understand it, because of using a more sophisticated structure than MD, its possible to do things like:
- shell completion can be generated automatically from the man pages.
- a website like mankier.com which renders man pages in HTML and adds hyperlinks every time an option or argument