I have similar feelings with music notation too. we never applied our "user experience" standards to mathematical notation and music notation. If these things were invented today, we might come up with better ideas. One painful experience I have reading math is telling which variables are "vectors" and which are "scalars". another is the similar looks of certain greek characters and english characters, such as alpha…
Also, in keys other than C, I felt that it wouldn't kill them to mark every instance of the sharp and flat notes, instead of doing it once at the beginning and implying it everywhere else.