In the IT world, the explanation for anything that seems incredibly inefficient or unnecessarily complex is: "Things are the way they are because they got to be that way."
Tradition (in this case Pythagorus's way of thinking about music and 2000+ years of theorizing, nomenclature, and teaching based on that) forms a gravity well that effectively prevents such changes.
It's much like spelling American English. Our language has 24 distinct consonant and 20 distinct vowel phenomes for a total of 44 unique sounds. Our alphabet only has 26 letters. And although our spelling is now "standardized," that standardization is arbitrary and based mostly on tradition and convention rather than on any sytematic appriach to spelling. And while it would make more sense to just create a better alphabet (several already have been created) it's a hard sell when everyone is already used to the dumb system we currently use.
So yes, shoehorning a chromatic well tempered twelvetone scale into a diatonic just tempered eight note theoretical framework (because the number eight had a mystical significance) makes little sense. If each tone had its own note, sharps and flats and all the confusion they create would go away. Key signatures would become unnecessay. And…the list of benefits goes on. But it ain't gonna happen.