I do believe in this theory but it is difficult to tell if it's intentional
There's quite a bit of stuff in this game that they do put in for fun. Case in point, the truck. Yes,
that truck. Did you know that Game Freak put it in Fire Red and Leaf Green because of the attention it got on the internet during the First and Second generations? Still doesn't do anything, but it's still nice that it's there.
I highly doubt that the lack of any Pokemon having the capacity to learn Transform, after them adding nearly five hundred species, is purely coincidental at this point. In Second Generation, Transform couldn't be Sketched, which WAS intentional. As of today, though, I am not sure if Sketch can be used to copy Transform, and Bulbapedia doesn't mention whether Sketch has ever gained that ability or not (like they mentioned with Self-Destruct and Explosion). I mean, it's fairly obvious though, that Transform is intended to belong just to Ditto and Mew (and Smeargle if it can, in fact, Sketch it). Even then, Smeargle has to learn Transform from either Ditto or Mew in the first place.
EDIT: As an aside, I tend to liken Smeargle's Sketch to that of Relm's Sketch from Final Fantasy VI. The Sketch isn't the "real deal" as it were. Instead, it's a life-like painting that has the mystical ability to come to life and do what it's supposed to do. Smeargle, in this respect, is essentially doing it the same way. He's using his "paint" (the goo that his tail excretes) to recreate what he's seen. In that sense, he's not really Transforming in the sense that his bio-molecular structure is recombining itself, but rather he's simply painting the effect of Transform onto himself and recreating the effect. At least, that's how I tend to rationalize how Sketch works in the pseudo-scientific way.
As for the theory itself, intentional or coincidental, it's still quite fun to think about.