A microcontroller and an Atom are very different things. The microcontroller is great at electrical interfacing, but terrible at anything processing heavy. The Atom is the opposite. Successful high-level system typically combine microcontrollers for the electrical signals, with high-power CPUs for the heavy signal processing lifting.
Regarding controllers "50 lbs+" says nothing, because torque is measured in force-times-distance, and you're just specifying weight (or, perhaps, force.) The thing that matters for a motor controller is the maximum current draw of the motor, which should be specified in the motor data sheet. You should size the controller for twice the maximum current, and twice the control voltage, because when turning around the power to the motor, you may temporarily see spikes that are twice your supply. Examples of high-power motor controllers include the Sabretooth line from Dimension Engineering, and the Roboclaw line from Orion Robotics. Both of those can be controlled from a PC or a microcontroller using USB or TTL serial. The Roboclaws also have encoder inputs and a closed-loop PID controller.