I have been reading the RM and various stuff online about this, and wonder what the issues are with PA0 if the 32F4 is not used in any low power modes.
On my board, PA0 is set up to be an input with a pulldown, but it otherwise unused because we could not work out the full extent of the limitations. I would like to use it with TIM5 (CH1, via AF2) which is handy because it is a 32-bit timer.
CH1 can be an input or an output so you can use it for PWM etc.