Change is not the same as progress. A lot of people are against change, for reasons both good and bad. I'm not familiar with the arguments over directory setup, but I'd almost bet money on them centering around tradition.

Personally, I think the various flavors of directory setup are already so divergent that tradition no longer holds massive value, but that's not something to be proud of.

How is OSX's directory setup more logical than the traditional Unix one? Be careful not to confuse your familiarity with one system with it's inherent qualities. I have switched between BSD an Linux as my main desktop OS a few times and had this "damn, this is so much clearer in x" feeling in both directions.