Well it's been said the Rinnengan are the strongest eye technique and the ninja that created the ninja world had them. However how many know of and fought against madara's super sharingan? If any it was the 1st hokage, and considering he was hokage, he must have won... so I would think that Pain is stronger just for that reason...
However madara does have generations of experience on his side, and possibly new techniques and/or eyes.
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