There are lot of things that needs a lot of research. Unfortunately, as we go deeper into money minded society, these things will get less attention and less funds. And, I believe there is no solution to such problem.
There was a time when accountants (or their more fashionable variant MBAs) were not in charge. Because it has happened it can, and likely will, happen again. Most of what we are experiencing is a hang over from the rise of the 1980s management consultant and the resulting private equity culture. It’s an emergent reality and isn’t structural.
I suspect that what makes protons and other quantum particles so difficult to understand is our assumption about time: that it's a level straight stream that flows forward, maybe with some minor distortions due to massive obstacles on its way. However at micro scale, this stream is probably very turbulent and should be modeled as multiple local streams.
Many tens of thousands of people have studied quantum chromodynamics (and related experimental results) enough that they understand there is a scaling problem in the proton: the more energy you use to probe a proton the more internal structure is revealed. We're orders of magnitude away from being able to probe proton structure at scales where "the problem of time" arises in any practical sense.
> "our assumption of time: that it's a level straight stream that flows forward"
That's not an assumption anyone who's studied physics would recognize, except (being generous) to the extent they read about the history of physical equations before about 1910 which were parametrized by "absolute time", and which have been superseded by relativistic equivalents.
There is no single "assumption" about time; time is treated very differently in different candidates for a fundamental physical theory (and differently again in theories that aren't fundamental; non-fundamental means that although bulk behaviour might be completely and accurately described, it emerges from microscopic behaviour not dealt with in detail by the non-fundamental theory -- examples include Navier-Stokes and Bloch's theorem).
Since no later than the second decade of the 1900s (in the aftermath of de Broglie 1923) it's been known that at some energy scale lengths and durations stop making sense, and since the 1970s (in the aftermath of Wilson 1975) it's been known why they stop making sense, from a mathematical perspective. In the 1960s, DeWitt (and Wheeler) were already pointing out that (as it later was proven) there is a problem with the treatment of the temporal dimension (and causal structure) in relativistic quantum mechanics. This has lead to more attempts at building new physical theories than you're likely to imagine, mostly but not exclusively in quantum gravity. It has also lead to considerable philosophy and foundations of physics work, largely but not entirely swept up in "the problem of time".
There is a huge body of related literature available for you to read at your leisure, and people who would happily engage with you and take your thoughts seriously once you're underway.
