You could do three easily enough on the Atmega328 (it has three timers). I'm not sure about 6 different outputs. Why six?http://www.gammon.com.au/forum/?id=11504
Can Arduino output 20kHz PWM with varying frequency?
I think that you're developing a variable-voltage, variable-frequency, three phase power supply, akin to a variable-frequency drive for a motor. Is that what you're working on?
Do you think Arduino Uno is enough as my interface?
... two analog inputs that can read 20kHz signal as feedback loop
The issue is not really 8 bit uC or 32 bit uC when driving 3PH transformer or motor.
I mean with few KVARs and KWs at frequency beyond 20 KHz.
see if I can go after 3 phase power electronic project