I actually have 3 big complaints with itunes/ipod.
If you browse away from the album you are playing, looking at other albums, or fixing/editing names, etc, it will stop playing the album, and you have to go back and tell it to keep playing. I find this incredibly annoying and stupid.
you can't delete songs within smart playlists. I understand why, cause it's only the playlist, but I want to be able to edit/delete duplicates of my recently added songs
if you add playlists onto your iphone/ipod, it puts the artist names of each track into your list of albums, even if you just have one song by them. Since my iphone has limited space, mixes and compilations make a lot of sense, but since I don't have space for the entire album the songs are from, it makes my artist lists completely unusable, full of 1 song listings. There should be some way to turn this off, like the group compilations option
there was one other thing, i can't remember. But generally I love how the newer itunes keeps music files organized. it's way less work than the older versions.