The missing feature I find most irritating is the lack of sophisticated paragraph and character style options. Normal text plus a bunch of headings isn't sufficient for the sort of documents I need to write.
My #1 complaint about Google Docs formatting is the lack of inline/block semantic code styles, and my primary complaint about Markdown is having to spam backslashes to escape variable names and math expressions outside of code blocks (I also wish it had multicolored highlighting like Google Docs, but that's just my idiosyncratic way of taking notes on code and color-coding values by type/origin).