I agree that progress in experimental abilities and QC is really forcing physicists to think carefully about what QM means. In fact the month of May saw three papers by major physicists about these deeper issues in QM [1,2,3] In my own humble capacity as a graduate student in physics, my research is about clearly understanding the divide between classical and quantum physics.
On the rewriting of theory, I should have been clearer. I meant that when you rewrite the theory you should think about ontology. Differences in ontology between different rewrites, as well as interpretations of those rewrites, will point to how quantum theory can be generalized.
I agree completely that quantum mechanics is taught horribly. Strangest of all are introductory quantum/modern physics courses that are meant to give students an intuition of quantum theory use the Copanhagen interpretation -the one that says the least about ontology and emphasizes calculations and empiricism.
I still stand behind my central claim. Let me be clearer. The mathematical model of classical physics says something about physical reality. The mathematical model of quantum mechanics says something very different about reality. Even if there are disagreements, we all agree that the ontology of classical physics is very much incorrect. Extrapolating from this I claim that the next theory of physics will have an ontology that will look nothing like that of quantum theory. As I have said previously, the ontology of quantum theory can be a means to an end (the next theory), but not the end itself.
[1] http://arxiv.org/abs/1405.1548
[2] http://arxiv.org/abs/1405.3483
[3] http://arxiv.org/abs/1405.7577