Matthew Thomas has listed 48 of OS X's shortcomings, and I've gotta say, he's spot on - from what I can tell. (I don't use Mail.app or iChat, so can't comment there.) A goodly portion are examples of Apple's own engineers ignoring the HIG and the frustrating inconsistencies found between apps. The bottom line:
Apple's human interface has declined and continues to decline. That other current platforms, both Free and non-Free, continue to be even worse does not make this situation any more satisfying. Mac OS X is like Sir Winston Churchill's description of democracy: the worst possible system, except for all the others.