Dear Armin,
Physics concerns what we can say about nature...just this philosophy is underlying the line of thought "It from bit", but I am convinced that we can know Nature's last secrets. To me the most promising way to unveil these secrets is a Modern Metaphysics, because the ONE (i.e. an omnipresent and transcendent field) is the most fundamental level of reality.
If we know how the ONE determines structure and conception of the universe we are on the path toward a final theory of the Universe. But the ONE implies a specific feature or attribute, that contradicts the possibility to state distinctions, because the ONE is explicitly defined as the foundational branch of reality, in which ALL distinctions are solved into Oneness. That's the inner meaning of the term - the ONE.
If information is introduced or implemented in physics as the most foundational level just this secret or hidden field of reality (i.e. the ONE) is, in principle, excluded. We are simply unable to see or to understand the 'meaning' of this field inclusive the meaning of the universe.
I agree with you that we need distinctions before we can have information. But if this is the case, the meaning (!) of distinctions within the global context of reality cannot be grasped by information itself. This seems to be a philosophical task - at least in parts. (Empirical data may be necessary to identify the physical distinctions with which Nature is dealing.)
By the way Wheeler's notion of "It from bit" is only half the truth: He often expressed his deep appreciation of the science of Einstein. The point of his appreciation was centered on Einstein's grasp of the importance of the WHY-question in physics. The WHY of the universe had to become vital for real progress to be made. Therefore Wheeler has called the scientific community to seek to do "Meaning physics" because of the importance of this point. We could not be content merely with knowing HOW the universe goes, but we must be able to penetrate into its MEANING, where both moral and physical laws are found inherently in the nature of the universe. It was just this kind of epistemology that was demanded by him.
I admit that the ONE and its relationship to the visible universe could not yet be clarified in terms of physics convincingly, but I am nevertheless believe, that the ONE and only the ONE is the key to a final theory of the UNIVERSE, because it answers the WHY-question.
Out of this epistemological view I am convinced, too, that a purely information-theoretic approach leads to a picture of reality, that is unreal and artifical. This becomes obvious if you look at the (Aristolean) relationship between substance and form. If this relationship is formalized in terms of bits you get a dead universe at the end - a universe, in which nothing happens.
I've tried to sketch this conclusion in my 2010-FQXI-paper "Can the Universe completely be digitized?"
To summarize my point of view: An information-theoretic approach is very modern, but it seperates us from the possibility to understand the inner meaning of the Universe.
Nevertheless, I wish you good luck with your paper. Though I do not agree with your position, I've rated it high, because it expresses the deep wish to grasp the inner core of reality.
Regards
Helmut