I would imagine that George Perez was put in a difficult position with Superman, because he can't really reveal anything about the present Superman without interfering with Grant Morrison's plans. That's different from when Perez relaunched Wonder Woman, because he had total control over Diana and how her character developed.
That would explain why he chose to concentrate on Superman's surrounding characters and their situations, where he would have a freer hand.
It's kind of unfair of DC to put creators in these difficult positions. That's why a full reboot would have been better. Then all DC comics could start at the same point and show how all these characters developed. This relaunch is sort of like One Year Later, where DC was being coy about the different heroes and their relationships--in an effort to keep readers guessing--but it's hard to coordinate that kind of thing across several titles.
DC set him and any future team on the book up for failure then. They should have had Morrison's introductory arc run through both titles with enough artists on standby to keep from getting behind schedule and quickly set up the new status quo.
These problems are only going to continue if Morrison and Morales fall behind schedule, as both have done so in the recent past.
Of course, DC screwing up a relaunch is a common occurrence.