Hello Diogenes,
I like to thanks you for having written this essay. I have found your paper original, profound and well founded. It makes many important points so fundamentals that have the potential to end the state of stagnation the physics is for the last decades. If I understood well, you say that eventually all physical theories will fail, because are built with "system bias" as a consequence on being founded on perceptive derived concepts. I would like that you had included an example of the reasons you think a specific physical theory, like general relativity, sooner or later, will fail.
You have proposed the existence of an ontological substratum of "subjacent fundamental structures generated by The Essence". That proposal remind me the implicate order of Bohm, the notion that there is a more fundamental reality that determines the intrinsic connections of processes in the universe.
One of your proposals for the development of science is to enlarge its field, through the study of those fundamental structures of ontological nature. If this realm is not subject to observation, I ask myself how scientific endeavors can be accomplished.
I have seen many theories of discrete space time, but not one, has been able to link the space structure proposed with the physical world as you have done. Another feature is the change of the traditional use of the distance concept for a more appropriate one, the Action Distance. Many theories only postulate the necessity of a discrete space, and do not provide justification for the emergence of matter. By the way, it looks as if you have done a mix of emergent and reductionist approaches.
One of the more amazing things you achieved is clearing the concept of Time. In fact, I do not remember another scientific coherent concept of time. Time is always presupposed, or circularly defined, e.g. it is what clocks measure. Time as a property of space is a revolutionary concept. In a certain way you reconcile two antagonist positions. In one hand are those who saw the contradiction between the parametric time of science and the perceptual time and try to eliminate it from scientific theories like Barbour and Rovelli and in the other, those that see time as universal fundamental, like Smolin. The distinction of "fundamental time" and the parametric time is revealing.
In your essay you affirm that the perception of time is relative. That one needs to perceive two sequences of events in order to experience time. But, if a person is shut away in a room with no interaction with the exterior world provided with a fixed electrical light and no change at all inside the room, except for the existence of an ornamental plant in a pot that grow, you would say he cannot perceive time, because there is only one sequence of events. I think you are wrong. In this scenario, one perceives change and abstract time from it. What he cannot have is a measure of time because there is no other process to compare with.
Another instance when you demonstrated your deep insights is in the section of Inertia, Mass, Electric Charge, when you define Inertia in a general form as " a measure of the inner complexity of a system" and Mass as a form of Energy with a complex (or compound) dynamic structure that confers it Inertia.