from how I see it the Rinnegan grants the owner powerfull jutsu, and with the connected eyesight a wide field of vision. but it has been proven that the rinnegan can not see through dust. so it is a powerfull eye. but it has no genjutsu ability's
however, the sharingan grants it's owner the ability to see chakra (remember sasuke vs deidara, the mines hidden underground, but sasuke could see them no problem) so he could spot nagato trough the dust. not to mention the ability to copy ninjutsu and taijutsu,and the genjutsu potential. and once it evolves into the MS there are also powerfull jutsu made available.
so if that MS is owned by a genius I doubt the rinnegan stands a chance ;-)