Dear Edwin,
I have just finished reading your essay for the second time, and I must say I am impressed. I believe you are absolutely correct when you advocate focussing on ontology in order to make progress in physics. Be sure to read Israel Perez's essay as he makes some very similar points.
As you may have noticed in Marts Liena's essay on the aether, where he quotes some work of mine on time, I also developed a time-energy theory seven years ago. It works best when there is a preferred frame - so in your essay example with the kiddie car in the railcar, my time-energy theory totally supports your observation re the stationary observer looking through glass walls.
The support of ontology in developing physical theories is that we help dismantle paradoxes. The twin paradox is easily explained without resorting to using 'space-time' in the answer, as Einstein did.
There are no time paradoxes in my theory, but it is best explained when an aether is considered as a preferred system of reference (borrowing that term from Perez). I liked your quote from Mermin "...the concept of time is nothing more than a convenient...device for summarizing compactly all relationships holding between different clocks."
It is a concept I hold as well, as I believe in an infinitude of clocks, (a clock being any defined volume of space, each with its own individual tick depending on the embodied energy of that space).
I am interested in the physicality of dimensions (as distinct from their mathematical being). I think I understand three dimensions of space, as that is the world I inhabit. However, I do not understand zero, one or two, or four or more dimensions of space from an ontological point of view. To my point of view there is only volume, down to the smallest of scales, and volume means 3 space dimensions. String theories propose multiple curled up space dimensions, (comes from the maths), but I have no idea what these can be, as in my humble view there are only 3 space dimensions, and anything curled up inside a volume must have some other property that defines it. I do not mind having other types of dimensions (time, temperature, pressure, energy, etc) as long as their meaning is made clear.
I like your point "I am ever more convinced that many of our nasty problems in physics have very little to do with the issues on which this essay contest is based", which is also made by Perez.
As my entry was my first ever FQXI essay, I tried to stick to examples of undecidability, computability and unpredictability, in my considerations of a TOE, although I do wander on to the philosophical time topic of presentism which I currently endorse.
I am currently reading some of your previous FQXI essays and look forward to further discussions with you. Good luck in this one, your essay is most interesting.
Lockie Cresswell