It was always gonna be unlikely that Amnesiac was gonna be more widely appreciated than Kid A. A minority might prefer Amnesiac over Kid A, but at the end of the day Kid A was bound to satisfy more people. The songs on Kid A are the first cabs of the rank, given greater regard by the band themslves than most of the songs from Amnesiac. They are ultimately all songs from the Kid Amnesiac sessions, and I highly doubt Kid A was released with the Amnesiac album (as it would turn out to be), in consideration.
What is most staggering is the quality of the third cabs off the rank, Fog, Cuttooth, Kinetic - all are cracking songs.