Because the lyric sheets had already gone to press when they made the decision. It was literally last minute. There were a lot of anomalies that resulted. First of all, Empty Spaces was supposed to be a reprise of the What Shall We Do Now, if you look on the lyric sheet, not only are the words different, but Empty Spaces occurs later in side two, I think after One Of My Turns. Also, Hey You was originally going to end side three, seguing out of Comfortably Numb's fade out. I can't remember if the lyric sheet had both verses to The Show Must Go On or not (it's one verse on the album, but when they played it live in 1980, at least, it was two verses).
Apparently, someone, presumably either Roger or Bob Ezrin decided side two was too long, so they cut What Shall We Do Now. I'm not sure if they thought it was too long, in terms of sound quality, or if it was just "too long for the listener" or whatever, I don't know. I always thought it was curious that when they played it live, they did What Shall We Do Now, but not Empty Spaces, which maybe suggests they felt that Empty Spaces didn't work as well in it's original place on the album.It also made the live performances and the film! The 'Empty Spaces' intro was kept but sped up to segue into 'Young Lust'. I'd have found another way of doing that and kept in 'What Shall We Do Now' as well...the latter lyric does delve into pointless rock star excess in a way that the other lyrics do not, so it fills a gap.
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