@ Rin, I'm still not convinced.
The previous clone, the first one that Tsunade destroyed thinking it was Madara, had a Rinnegan. The rest probably had it as well, since the whole shared vision is useful and would give Madara better 'sits' to watch and 'enjoy' the battle more.
This page suggest that you can't cast genjutsu from Rinnegan, that it is one of the distinctive abilities of the Sharingan and what's more, it suggests that the Complete Susanoo, is actually an ability tied to Rinnegan as well (would make sense, since So6p would need to hold the Jyubi somehow, until it was sealed in him). Not to mention that probably the other eye was still a Rinnegan:
For the same reason Tobi is using both, the Sharingan and Rinnegan, since there are still some abilities that can't be used from Rinnegan alone.