ATYCLB is a more joyous sounding album, more uplifting and hopeful, with songs like "Beautiful Day", "Elevation", "Stuck...", "Kite, and "Walk On". These songs have a common theme - one that even in times of despair, there is hope.
HTDAAB starts exploring more serious issues again - issues of being lost, trying to find one's self, issues of loss, of war. So even though some of the sounds are similar, the lyrics and themes are almost at polar opposites.
WITS is a light-hearted love song. It discusses that even though a relationship was severely damaged, there is hope, and that love provides that promise. As such, this song easily belongs on ATYCLB. Musically, it may arguably flow on HTDAAB, but thematically it fits on ATYCLB. One could even argue that if not for the very pop-sound, it could even be on AB, which is an album that really explores all aspects of love.
However, as it's on "U218", I'm not disappointed. I think of this as a bit of a throw-away song. It's cute, it's light, it's a love song - it's perfect for a greatest hits type of package.
Also, I agree with BonoChick - thanks to iPods (iTunes), CD-R's and tapes (what are those?), people will create their own special U2 songs mix, which may or may not feature WITS. So it really doesn't matter much.