A big part of the problem is that most music theory was developed to describe preexisting practice, without a whole lot of knowledge about why tonal music is pl

A big part of the problem is that most music theory was developed to describe preexisting practice, without a whole lot of knowledge about why tonal music is pleasing. The result is a music theory that's highly layered, with the layers corresponding roughly to the major quantum leaps in theory all mixed together, rather inconsistently. We could go back and fix it, but that would require a grand unified theory of harmony, something which hasn't quite emerged, although we've made some big steps on the past decade. The other reality is that we tend to teach theory from a perspective that explains simple music and progresses to the more complex, and then chronologically. This may be helpful for practicing musicians, but it does little to explain how the fundamental tonal concepts for together (scale structure, harmonic progression/voice leading, timbre, and tuning).