Aside from perhaps images, I wish that browsers didn't try to render more complex content. I'd much rather be able to easily watch YouTube and embedded videos, for example, in an external player. And I've almost always ended up reopening PDFs in an external viewer, or configured the browser to do that by default where that option exists.

Maybe Markdown isn't as much of an issue as the videos and PDFs are, but it seems to me like it's better handled externally from the browser, or perhaps by an optional browser extension.