I think the big hole in our physical models is the formulation of time.

As mobile organisms, we experience our environment as a sequence of perceptions, in order to navigate, so our concept of time is as the point of the present, moving past to future. Physics codifies it as measures of duration and treats it as a dimension, or timeline of events.

The reality is that change turns future to past. Tomorrow becomes yesterday, because the earth turns. Duration is the present, as the events coalesce and dissolve.

There is no actual dimension of time, because the past is consumed by the present, to inform and drive it. Causality and conservation of energy. Cause becomes effect.

Different clocks can run at different rates because they are separate actions. Think metabolism.

Time is asymmetric, because it measures action and action is inertial. The earth only turns one direction.

Energy is "conserved," because it manifests the present, creating time, as well as temperature, pressure, color and sound. Time is frequency, events are amplitude.

Energy, as present, goes past to future, while the patterns generated go future to past. Energy drives the wave, while the fluctuations rise and fall.

Consciousness also goes past to future, while the perceptions, emotions and thoughts giving it form and structure go future to past. Though it's the digestive, respiratory and circulatory systems processing the energy and feeding the flame, while the central nervous system sorts through the information precipitating out. Thus the intellectual attention to patterns and information, over the dynamics underlaying them.

Even galaxies are energy radiating out, as structure coalesces in.

So look back over the entire field of modern physical theory and you will find this seemingly detached modeling, that keeps having to add ever more fixes, particles, dark matter and energy, etc. Almost like epicycles all over again.

One way light does redshift over distance, is as multi-spectrum packets, as the higher frequencies dissipate faster, but that would mean we are sampling a wave front, not observing individual single spectrum photons that traveled billions of lightyears.