I've been travelling enough recently that I've gotten quite bored of the music that I've had on the iPhone since I got it…but iTunes is such a pain to use that I don't update its library anymore, and therefore don't sync the iPhone.
Apps that just read the folder structure are so much more logical, and so much easier to use. Audirvana is my current one, with a very nice extended metadata editor built in and, of course, support for FLAC.
Will Apple ever sort this mess out?