Pain was essentially the face of Akatsuki. He was the one who led the organisation, and he was the one practically all members accepted as their superior. But in actuality, it was Obito who was pulling the strings - it was he who commanded Nagato to hunt the Kyuubi, even telling him that as leader, he wouldn't accept failure. So in essence, Obito was the leader, but only to Pain directly (and indirectly to the rest).