Dan,
I just read your essay, which I found very well written. A couple of things came to mind:
1. I agree that it's optimistic to expect nature to have a bottom to its complexity. Nevertheless I, and many other people, like to speculate about what such a fundamental level might be like if there were one. I think this is OK because physics is inherently optimistic; we assume we can make some sort of sense out of the world. Once you grant yourself that, there is no limit to human ambition. However, each recent generation of scientists has made fools of themselves by assuming they were near the bottom!
2. I would hope that we as humans can modify our thinking and approaches to nature in response to what nature throws at us; in other words, I would like to think that physics is more about our ideas being modified by what we learn than about us trying to put nature into a straitjacket. Quantum theory, for instance, was mostly forced on us by observation. The human insistence that the world be commensurate with rational thought, which you view with skepticism, seems to me like a moving target, because our ideas of "rational thought" in relation to science change whenever nature hits us with something we don't expect. Of course, it's possible that humans may be incapable even of asking the important questions; we'd never expect a rabbit to be able to ask the important questions, and are we really different from a rabbit in the grand scheme of things? I think so, but my view is hardly unbiased.
Anyway, it was a great read. Take care,
Ben Dribus