I considered that, too. Whilst the shows on the North American leg of the tour saw some fine performances of the end section of Supper's Ready, by the time the band reached Australia, there were clearly some vocal problems which resulted in the song being replaced with Afterglow.
Phil has always said he enjoys singing Supper's Ready, though, and has no issue with fans considering it to be the best thing Genesis ever did.
On the WCD tour, Phil caught a cold which resulted in a concert in Miami being cancelled. Subsequent to that, he lost a lot of his mid-range and Mama had to be dropped from the set. By the time the tour reached England, his vocals didn't seem as powerful as they used to be, although he still gave it his all on stage and some of the melodies on stuff like No Son Of Mine and Home By The Sea were sublime. After the stadium tour, Genesis did an "encore" tour of smaller venues throughout Britain. I caught the band at Earls Court and Phil's vocals were still in good shape.
That's something I never considered: The difference in vocals necessary between a stadium and a more intimate venue. I caught two WCD shows in Philly on back to back nights. After a little research (and The Movement live database), I found that they did not perform the TIOA medley on the first night with a report from an attendee that Phil sounded "off." I remember the 2nd show being the better of the two.
From what I remember Supper's Ready was off the table from the get go on the 2007 tour. Never heard the reason. I kind of remember reading something from management saying, "No Supper's Ready, so don't even ask."