Pain was the strongest in Akatsuki PERIOD!
Obito is not above him. No one in Akatsuki can ever stand up to his Six Path's at full power.
Don't overrate Kamui, it can be almost flawless if it was in the hands of a master. But Obito is far from one, he's been hurt too many times and has even come close to dying. He's too arrogant and clumsy, although I doubt he would underestimate the Rinnegan and risk any carelessness. He still wouldn't beat Pain.
Pain was number 1