The two things I wish mediawiki had:
* 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.
What it does right is that it's trivial. Trivial to understand, trivial to use, trivial to upgrade, and trivial to write plugins for. These plugins can then suck in data from external systems and CMDBs which is perfect for internal documentation. Mediawiki is designed for another use case and much more complicated.