This is a very difficult fight to call seeing as we know very little about the full extent of both of their abilities.
Madara does have EMS and a pretty haxxed space time ninjutsu however he cannot summon Kyuubi so that would be a huge chunk of his arsenal taken away. Madara has also been defeated in the past and his list of failure spans almost a century.
Pain on the other hand does possess what has been stated as the strongest doujutsu and has never lost a battle. In addition he defeated Jiraiya fairly easily when he got serious. With 6 bodies and the ability to fully manipulate all 6 elements, he is truly a formidable opponent.
Based on these arguments Pain should win. However he doestake orders from Madara so I'm not so sure. All of this is speculative anyway.
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