* APIs with deeper functional inroads in multiple languages. There are lots of great tools for writing bots, but if you want to write a parser extension, you're stuck with PHP right? Or has that changed?
* Multiplayer. Edit conflicts can be a real pain and turnoff for beginner users. I wish that simultaneous use felt more like a collaborative social experience and less like a minefield.
...but I do think mediawiki is wonderful, and I'm inclined to use it despite these drawbacks.