Basically, Nagato has the ability to use all 6 elements if he wants to. He could maybe even use 3 together if he's good enough. That's what the Rinnegan and the whole sage of the 6 paths thing does for him.
Says 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.