I think a valid comparison is the regular alphabet. It is, after all, a coding system for language in the same way that notation is a coding system for music. Most of the problems of that coding system (my pet peeve is english spelling) generally stem from conventions rather than problems with the alphabet (italian and german is much easier to spell correctly).
There might be some interesting alternatives (hangul!), but those systems come with their own share of problems and generally have no big benefits. I actually believe that musical notation is better fit for it's task than our current coding system for language.