It's very difficult to say who would win. I'm sure that the Rinnegan has abilities equally as dangerous as Amaratsu, Susuanoo, Tsukiyomi, and Kirin. Itachi' genjutsu would play a major role in this fight since we know that Pein is vulernable to the art. By wearing one by down using the technique, Itach can give Kakashi just about enough time to use his Mangekou Sharingan ability and permanently remove one body from the the fight.
When the other bodies show up, it will be up to Itachi to use his Amaratsu in order to permanently annihilate a a few of them (I think he's in for about two shots). Sasuke would serve as a very good offense once Pein's chubby body is taking out of the picture.