The place where I see the problem/wrench is in the claim for similarity between ontological development and scientific activity of generating and testing hypotheses.  What you say at the end of your email (about the gene mapping) does that apply to, say, going from Newtonian physics to relativity physics or to quantum physics?  If so, are you saying that the progress of science is not qualitative in the sense that Piagetain ontological development is?  If you are taking such a position, then I think you succeed in avoiding the problem I find in Piaget--who I read as holding to more similarity than that between the ontological development and progress in science.   

I actually hold that there is qualitative change in both cases, but that there is still not as much similarity as Piaget seems to me to claim. Here is why:
You say "The epistemic being has to equilibrate not just the internal structures
between themselves, but also with the environment/world/universe."  Fine.  But I want to focus specifically on how that double equilibration comes about.  I claim that for Piaget it comes about through some sort of phenocopy mechanism--the mechanism of generation of the new structure is such as to ensure that it copes better with the external world than do the earlier structures from which it derives.  I hold that this is  built into Piaget's theory of equilibration.  And I hold that this is very different from what happens--according to a common view -- in the progress of science--where the generation of new theories is not constrained in this way, the constraint coming afterwards in a separate selection process.

In my own thinking on the difference I see between (a)  Piaget's ideas on ontological development and (b) that common view of scientific progress, I move in a particular direction.  I tend to think that Piaget's view of ontological development would benefit from significant modification in which phenocopy ideas are largely replaced by ideas of generation and selection similar to those seen in scientific progress.  (I have argued for this kind of modification on other grounds in Becker, J. (2004). Reconsidering the role of overcoming perturbations in cognitive development: Constructivism and consciousness. Human Development, 47, 77-93.