Dear Jose,
If existence of matter can be considered as a fact, rather than an assumption, I would say that no assumptions are required in physics. All physical phenomena can be logically explained on the basis of this 'fact' (of existence of matter) alone.
However, a fact (I believe) is nothing but a statement that is believed to be true. An assumption is also defined in same terms. Once you know matter for a fact, why assume its properties. Properties will be self-evident in definition of matter.
[Mass is a measure of inertia or it is a mathematical relation between matter-content and change of state of motion of a matter-body. Matter, being a single type of entity, a matter-body cannot have different natures for its most-fundamental particles. There is no unambiguous definition for 'energy'. Whatever energy means, it has to be distinct from matter and hence, they cannot be converted/reverted into each other.]
I think you presented a brilliant analysis, in your essay, of current affairs in physics and your suggestions on ways out of present dilemmas are very practical. Nevertheless, who will bell the cat?
With regards,
Nainan