Confluence has two main advantages: It's very fast to create/edit pages, and it has a hierarchiecal page tree to organize information logically.
ProHierarchical page tree
ProEasy to use
ConRedesigns are rolled out without thorough testing
ConMany unresolved bugs
ConSearch is utterly terrible
I personally see Markdown as too much of a mess with different incompatible flavors. Using double whitespace at the end of the line as a hard linebreak is also something that I don't like. There's no unified standard.