Madara could never have been the true leader if Pain stood up for himself. But Madara had him convinced that he was so much smarter than him, the Pain was right to follow him. If Pain hadn't been manipulated he could not only have ruled Akatsuki but the entire world. I mean he has a Kekkai Genkai that can use every single jutsu in the world, even the sharingan's copying can't use special natures and kekkai genkai.
Additionally he has the power to bring the dead back to life in full, not imperfect necromancy like Orochimaru either, but genuine control over life and death. He was basically a god. He would have been the greatest ninja of all if he had a stronger will and wasn't constantly following others.