Do you have any knowledge about those protocols? If not plz visit youtube there are a lot of content, eletronoob has also covered this topic. Then it will be better to judge for you.
Ppm and pwm are not much different control signal protocols the fist attention drawing part is ppm is less clumsy as it has only 3 wires Signal Power and Ground
And it can handle multiple channels according to the maker
But for pwm each channel requires individual signal cables if the Power and Ground are common.
So it will be better to stick to ppm , also the drone you are building will easily process it as its based on multiwii
But beware the motors dont process ppm ..dont wary the flight controll will convert ppm to pwm for motors.