Just for plot purposes. From the moment Tobi was introduced and so quickly after Obito there were people saying they were one in the same. It may have been just the two of them but given the circumstances they had to be careful. Imagine if Dederia popped up in the cave instead of when they found his arm? It'd through everything out of sync.
Pain was the visable leader or puppet. His job was to be the one everyone saw and rallied around, but it limits what you can do. By operating in the shadows Obito/Zetsu can watch and make adjustments to Madara's plan while using Pain as a pawn. It was actually brilliant by Kishi to have the placing like that.