There is only one, U3 is the controller. U2 is LM339, you can see the chip marking if you shine a light on the chip at an angle.
From what I remember when I traced the signals, each of the 11 LEDs connect to the mcu. 3 switch, 6 motor driver, 3 bemf, 1 current sensor, 1 voltage detector, +5, gnd. that's 27 pins. I can't remember what the last pin connects to.
So in order to get the same functionality (or to use the same size board), the replacement mcu must have at least 26 IO lines. Plus a pwm and a direction pin, that's 28 IO lines, more if you want more functionalities. So an atmega328 will not work as replacement. But if you want no frills simple controller that is controllable by pwm, then atmega328 will work just fine. I plan to build a no frills one for starters.