IF those fans are pwm, you'll have a hard time with a controller, since the pwm signal is generated by the motherboard. That means, to control individual fan speeds externally from the motherboard, you'd need someway to either generate a pwm signal, or change the signal. Changing the voltage of the fans won't work as they need the full 12v to operate correctly when used with a pwm signal. Pwm is pulse modulated, it's constantly in a state of trying to turn on, but never getting there unless set for 100%. If you lower the voltage, the motor doesn't have the power to 'kick start' the fans, so will either draw more current to do so, or fail. This is why hubs are used, it's a constant 12v supply, the pwm signal is shared by every fan. There's no individual control other than by seperate headers, which are controlled by the bios.
It's one of the few advantages a DC fan has, a simple resistor or rheostat will change the 12v, so individual fans can be controlled, usually 5v or 7v low. Pwm use a digital pulse instead.