I'm pretty sure Jiraiya said that Nagato was able to learn *all* *6* ElementsSays who? None of the Pains have used any elemental powers at all. He has 6 different powers. Nobody said he can use 6 elements(which, like Buff said, there aren't even 6).
So...AGAIN...way to try explain away the animators plot holes by pulling powers out of your ass.
and if Nagato is able to use all 6 elements, then there is absolutely no reason for Pain not to use them too, because after all, he is controlled by nagato's CHAKRA.
problem solved! no plothole