maybe madara is the one who taught Pein all his current super attacks, maybe thats where their difference in rankings and chain of command comes from. Maybe Madara is the brains of the operation and Pein is just the arms and legs. Afterall even Itachi isnt afraid of him because he thinks of Madara as a worthless shell.
If you want to talk about the original Madara then thats something else. The current Madara, eeeeh not that so much
My fellow Naruto fans, I really really want to vote for Madara, but unless he can prove it to us, i cant really say.