At the risk of heresy, I prefer apple lossless but for one reason - that could just be me being an idiot.
Metadata.
Whilst the quality of FLAC is no doubt fab, I always find it a pain as you have to spend what can be ages putting in the metadata for FLAC files in iTunes, whereas apple lossless usually comes nicely bundled with track order and names, and often a cute little bit of album art.
As I say, this may be a non-issue due to me being a dolt, or there may always be those who value convenience of metadata over quality of audio.
So perhaps both formats is the answer for those who can be bothered.