Nic mentioned before the tour that he had practiced at least parts of Watcher of the Skies and Supper’s Ready. My impression is that they were at least considering those songs but set them aside due to the difficulty in playing songs like that for the first time in 40 years.
They rehearsed them right at the beginning. No visuals were ever designed for these and it's unclear how long the band spent on them. Possibly as little as one or two tries. Mike and Tony have both stated that they sounded "too old" and the idea of playing them was dropped. They also tried The Musical Box.
Didn't seem to be anything to do with them being too difficult to play. The band just decided they didn't fit with the rest of the set.
I was a bit surprised that Apocalypse in 9/8 didn't emerge, because Nic stated two things in several interviews....that he would only mention titles of songs that made the set and that he specifically enjoyed Apocalypse. But it now seems it was dropped after the very first rehearsal dates.
You and I may well feel this is a shame, as opening to Watcher and having Apocalypse in there somewhere would have been magical...but if they specifically didn't enjoy trying them out, we can't expect them to appear.
I would love to be proved wrong and for Genesis to play themselves out at the O2 with Watcher or Apocalypse. But I shall not be holding my breath.