I'm not sure the comparator will work with solar panels. I think of solar panels as current generating devices. So long as there is enough sun on the darker panel that its open-circuit voltage is at least as high as the voltage the brighter panel is currently operating at, then the two panels will have the same output voltage, but one will be producing far more current than the other. If that's correct, then comparing voltages won't really work. In fact, variations in the output diodes might result in the panel in shade having a higher voltage than the one in sun.
Edit: However, the fact that the forward voltage drop across the diodes increases with current may allow the circuit to work.
Can you explain what the Arduino will do differently depending on which panel is in shade?