Dear Chi Ming:
(A note to others: This conversation started in the forum of Julian Barbour's essay.)
We seem to agree, at least, that the concept of time is useful, which is the primary issue.
From your most recent comments and your essay, it also seems clear that what you are asserting is not a "paradox", but rather unscientific practice. Science is based on reproducible observation and you are claiming that scientists are adopting an interpretation of smooth time evolution, without observational evidence. This is a point worth exploring, but it does not involve a paradox.
I think that your essay is a very worthy effort. What I think you are doing, though, is creating your own interpretation of quantum mechanics. To wit, you say, "But we can generalize this and postulate that indeed ALL forms of energies can be interpreted this way, even those that aren't usually associated with QM." This may be the most sensible interpretation; I don't know, since I am not familiar with all interpretations. It is a great accomplishment to construct a new interpretation of quantum mechanics, and I applaud your effort; but there are assumptions in your interpretation, just as in the others.
You have asked me to give you evidence that time is continuous; but I don't have to do this, to support the position I have taken thus far, which is agnostic. I have not said that you are wrong; I have only said that you should provide observational evidence, before I say you are right.
But now, let me give you two reasons to believe that there is time, both between measurements and wave-function collapses, and also between the moments dictated by the frequencies of your 1-particle systems (at least in light of the issues you have raised so far). First, I can make a measurement any time I choose; you have not said that there is some minimum time interval, like the Planck time, that restricts my choice (the moon is always there, whenever we choose to look at it). Second, if I have two systems, at some start time, and I choose to measure one and then the other, there is a time for the first measurement, between the start time and the second measurement. Adding more systems, I can subdivide time into smaller and smaller increments. In an infinite universe, I can make delta t arbitrarily small, as the number of systems goes to infinity (note that I can do this with a countable infinity), unless you *assume* that only measurements by sentient beings collapse wave functions and that there are only a finite number of sentient beings. Similarly, between any adjacent moments of your 1-particle system, I can go out into the universe and find a system with a moment in between. Iterating, I can again make delta t arbitrarily small. Indeed, since you have not even asserted a minimum time interval, I don't see that discontinuous time follows from your model. And even if you were to assert, for example, the Planck time as a minimum increment for moments of a 1-particle system, your model does not preclude another system from having interpolated moments.
Finally, you stated, "The development of 20th century physics has taught us that what's not directly observable should not be treated as real. Such is the case for the ether..." (Did you notice, from my essay, that I am an Ether theorist?) It is true that many take this point of view, but I don't agree with it. For example, the twin paradox, of Special Relativity, is a true paradox, contrary to what is almost universally believed. Most have been convinced that it is not a paradox, because they think that there are no observational consequences. But, can you tell me which of the twins is older, after they part but before either makes a turnaround acceleration? If you believe in Special Relativity, you cannot; but, if you believe in the modern Ether theory, often called the "Lorentz-Poincaré Ether Theory" (LPET), you can. Moreover, in my essay, I discuss situations in which the paradox would become observable, eliminating Special Relativity as a viable theory. And, in fact, I have put forward a practical experiment to observe the ether of LPET, which is the state of rest, only with respect to which light travels, with the same speed, in all directions. My assertions are most falsifiable, unlike those in any other essay I have read in this forum.
Take care,
Ken.