When I import my music folder, iTunes copies all the files to it's own private directories, using the filesystem as an index. Thanks, but my music is already arranged the way I like.
iTunes doesn't play flac or ogg. And when I rip a CD, it wants to save it in some proprietary flac-like format (which, as far as I know, does not work on non-macs).
I enjoy controlling my music from a phone/tablet/other computer. Shameless plug: http://github.com/stucchio/DJ-Pirate http://cims.nyu.edu/~stucchio/software/djpirate/screenshot1.... http://cims.nyu.edu/~stucchio/software/djpirate/screenshot3....
iTunes + iPod also has some extremely unpleasant anti-features: http://support.apple.com/kb/ht1202
(Note: this may not all still be true, haven't used iTunes since 2007. )