What I didn't like about iTunes was the lack of customization. I'm not talking about skins and crap, because I've gotten over caring about that stuff as much as I used to, but I mean as far as aspects of the functionality. I like programs that have tons and tons of things to check and uncheck in the 'preferences' window XD I have no use for anything CD related so that never factors in when I choose my media player, either.
As far as file formats, the only audio format I have is mp3, so I never have to worry about that.