Can an Arduino Micro receive commands from another microcontroller when hardwired together? I plan to build functioning reaction wheels, controlled by an Arduino Micro. Ideally, I'd like to have the reaction wheels, and the micro, be a single unit which would receive external commands from another microcontroller.

I know you can link Arduino microcontrollers, and every time I've seen it done it has been with a RC module such as XBee. Is it possible to link units using something like the micro-usb on the Arduino Micro?

If this is possible, is it as simple as connecting the micro-usb ports on my microcontrollers, and then working out the programming?
You cannot do this with the micro USB ports.  You will need to use I/O pins.  Either serial or I2C would be good options.  It might be advisable to use I2C if you want to control multiple 'slave' microcontrollers as they can all sit on the same bus.  Using the serial port would require multiple transmit and receive pins on the master controller, likely requiring software serial ports (high overhead).  Also, if you don't use the serial port for comms, then you can use it for debugging.