Well you have to put into perspective a bit. Take all the techniques that we have seen, all of these have been fairly unique and exclusive to one person (except susanoo I guess). So whilst the sharingan as a whole has lots of different techniques, not every sharingan automatically gets these. So for the most part someone with the rinnegan will beat someone with a sharingan 99% of the time.
The other 1% is when someone like Shisui and his KA come along. Even than it's not confirmed how the rinnegan reacts to visual genjutsu but I would say shisui should win (but i'm not 100% on this). Even than it he would have to have not been in a life threatening situation for 10 years so the jutsu is available to him. It isn't a garenteed win for shisui, only if the conditions just happen to line up perfectly for him. I still reckon sasuke or Itachi on their own would lose to Nagato. Madar doesn't really count since we haven't seen much in the way of his EMS and he has rinnegan anyway.