Taking Radxa ZERO as an example, here are somethings to consider when you need to pick a GPIO pin:
1. If you plan to use a pin as another hardware feature (i.e. SPI/I2C/PWM/etc), then it CANNOT be used as GPIO.
2. Generally, ADC pins CANNOT be used as GPIO (pin 15 & 26). Not the output at least.
3. Avoid pin 8 & 10, since they are the default debug console, and many software parts assume they are available.
4. Avoid pins that is only available on a specific hardware revision (pin 35 & 38) to allow more sourcing flexibility.
5. Avoid OD pins (pin 22 & 36) since they require additional circuit to function like a normal GPIO.
Now almost every guidelines above can be violated given enough development resources, and they are ordered by the effort required from the most to the least. But if you are already considering to go against #4 due to the lack of available GPIOs, you might want to include a I2C/SPI GPIO expander and save the headache.
