let's answer ur question:1. Who said Pain obey to Madara?
Madara is Mastermind in Akatsuki,hes the founder! Is it so hard to understand ? Pain thinks hes most powerful,A God,why would he resist to go capture 9-tails,its fun for him,hes not afraid of anything.
2. Did we saw what real Pain/Nagato can do with Rinnegan? All we saw is 6 dummys with copied eyes-which can only do is-share field of vision.
Wait till Kishi shows "original" Pain and then say Sharingan is weaker/stronger.
1: Let's put u in the situation... I'm madara and ur Pein. I come at ur ''house'' and tell u that I want u to go on a mission that is certainly dangerous and that u have to success ur mission. To me, just to me that sound like a boss speaking to his worker... If Pein was the leader he shouldn't have needed the order of madara to go after the 9 tails!
2: Well if like u say the Real Pein is so mighty powerful, why don't he comes out? I'm going to tell u, because he know that even with his real body he can't win, so he won't risk his life in an attempt to kill madara! Seriously, Pein think of himself has a god! How could a god accept to receive order! He know he's no match that's all.