Essentially, yes, my theory is just a explanation for Mew's existence, pieced together from the clues the canon has given us. And say what you will about temporal loops, they're perfectly logically consistent and possible within quantum mechanics and advanced physics. You basically answered your own question with the reference to multiple universes and such; basically, not precisely. A temporal loop in this instance would require for Mew and Ditto to have come into existence simultaneously, in different times; since Mew has the ability to traverse time at will however, it technically exists (or has the quantum potential to exist) at any point in time.
It's rather complicated, but essentially, Mew being timeless is not equivalent to being eternal: it exists throughout the history (past, present, and future) of the Pokémon universe, however that does not mean that it lacks causality. However, though Mew is timeless and therefore its relation to time as we understand it is very radically different from what we experience, it remains perfectly reasonable to suggest that its causality can be traced to a point within the temporal dimension as we know it. It's not easy for a human mind to comprehend, but it is physically possible for something which is timeless to have originated as something which was within time. And from there it's entirely possible that it could have essentially "created itself" (i.e., ensured its own existence by forming a temporal loop, rather than perhaps diverging and passing into a parallel dimension or universe). It's actually a fairly simple and elegant concept, hard as it is to actually grasp. A cyclical causality: Mew exists and travels through time to be scientifically studied so that Ditto could be created so that it could cause Pokémon to hybridize so that Mew could exist and travel through time, etc., etc.
Your quandary essentially seems to be with the problem of "which came first": however the concept of a temporal loop/cyclical causality eliminates the need to answer such as question, since both "ends" of the loop (Mew and Ditto) exist simultaneously. Hope that clarifies a bit, but again, it's a very complex concept. However, it is likely one that the folks at Game Freak may have actually come up with: there are hints related to time, and to cyclical time, throughout the canon. Just because the concept is rather convoluted and difficult to understand doesn't mean that they may not have intended it that way: frankly, the concept's complexity only gives them a reason not to describe it in great detail (would you really expect children to understand something as complicated as this? they were the original intended audience, after all). Pokémon includes many complex subjects (war, reproduction, technology, etc.), but for many of them, they keep the details to a minimum in the canon: presumably for the sake of the kids, who might shy away from a game that included lengthy tracts of complicated or educational material.
Anyway, you know my theory. I don't think it's too complicated to be true, and I think the evidence ultimately leads in that direction. But to each their own of course.
