The only real thing missing is quite hard - an ability to do realtime I/O control. That's not really in the Pi, but the Linux OS. If there were a good realtime option, then the Pi would be an awesome controller (e.g. for 3d printing, CNC, etc.). As it is, you need an Arduino control I/O so you have precise timing, which adds complexity as you have to program two devices to coordinate, which is much harder than one. Not impossible, obviously, but simpler/easier is better.
I would add ADC would still be missing to make a complete controler wich is the other thing the arduino is doing on a 3D printer (for temperature measurement)