I've always felt that music is something that's constantly in development, and the theory of it tends to lag somewhat behind its usage. No one (at least, not many!) writes the theory before the music- they write the theory later to try and describe the music. We have a tendency to think of musical theory as something static and unchanging, when in fact its completely the opposite. The development of music can more or less be defined IMO as the breaking of the last generation's set of rules, and this accounts for a lot of the anomalies etc.
That said, my favourite (or least favourite, I suppose) is the idea of transposing instruments (horns in F, E flat trumpets etc) when we now have a prefectly good trumpet (or horn, or whatever) capable of playing all 12 notes equally well. It just seems totally redundant.