For example, we assume that arbitrary arithmetic takes constant time. Good. Except that if you take that seriously, then P=PSPACE. So we might say that bit operations on fixed registers are constant time. But nobody does that because then arithmetic is O(lg n) and it's too much trouble to keep track of everything (and if you do, then hashtables aren't O(1) any longer!) If we are more sophisticated we might take a transidchotomous model, but that's really weird and we have results like sorting in less than n lg n time. Not to mention that the mathematical foundations get a bit shaky with more than one variable.
I think the hard problem underneath is that it's hard to define a computational model that (a) can be reasoned about and isn't extremely weird, (b) has solid mathematical foundations, (c) is reasonably predictive of real world performance, and (d) is not linked to a specific architecture. Asymptotic analysis is kind of a compromise. It can be formulated in very elementary terms, it makes mathematical sense and if you plot the performance of a sorting algorithm on a chart it kind of looks like the graph of n log n if you squint a bit.
Knuth does something similar to what you're suggesting IIRC, albeit without the analytic combinatorics machinery. For some programs he derives a precise expression as a function of the size of input that describes how many operations of each kind the underlying machine will perform. In numerical analysis there is a similar concept, e.g. evaluating a polynomial with Horner has the same asymptotic complexity as the naive method, but we say it's better because it takes exactly the optimal amount of floating point operations (and, in practice, because it uses fused multiply-adds, but that's another story...)
A research program along those lines would be certainly fascinating, but the combination of "needs to be reasonably predictive" and "needs to be portable" is a tough nut to crack.