An interesting theory but a theory nonetheless. The notion that Zetsu has his own goals and ambitions almost goes without saying. So far, almost every member of Akatsuki has had their own goals and ambitions, most of them didn't even know what Akatsuki was really for at all. The question really becomes what is the extent of those goals. I think it is interesting to note though that Zetsu is one of the first Akatsuki members introduced and seems to be one of, if not the most, informed of all. Zetsu shows up at most of the major battles since the time skip. He essentially knows all the players and seems to be one of the most mysterious characters of all. Yet while he could very easily be far more important than he seems, it is also very possible that he is not.
In a many ways, Zetsu reminds me of Kabuto. For a long time I was convinced that Kabuto was playing Orochimaru all along and that he was a far bigger player than he was letting on. Kabuto seemed to have his hands in with everyone and always seemed to have an ace up his sleeve. He was cool to a fault and hinted like everything was going according to his plans. In many instances he appeared to be in a position of superiority over Orochimaru and Orochimaru seemed to rely on him in almost everything. Kabuto could have quite easily been the master of it all but that theory turned out to be incorrect. I think the same could easily be true with Zetsu. It wouldn't surprise me if he turned out to be playing almost everyone but just as was the case with Kabuto I have a feeling that for the most part he really is a subordinate.