Can be lots of reasons depending on the micro controller:
-analogue ground and digital ground for seperating the supplies
-bonding wire can handle lets say 100mA and the microcontroller has to be able to sink on all GPIO pins a total of 200mA (fill in any value you like)
-layout of the silicon, two groundwires easier layout (for instance power for the core and power for peripherals) or lower impedance.
and lots more,
two is not much, there are plenty of chips (like fpga's) that have more then ten ground connections and different power pins.