I'm sure someone could provide a link to multiple computer rankings about SOS to quickly end this debate. Common sense, though, at least IMHO, would point almost unequivocally to Iowa State having a tougher conference schedule.
However, there is no way to say for certain Iowa State would or would not have won more or less games swapping schedules with Iowa. That's largely due to the fact a lot of Iowa State's issues last season had more to do with Iowa State than it did their opponent. I would cite Oklahoma State and Kansas State as prime examples.
One of the biggest misconceptions people have is that Iowa State was a bad team last season. The results were bad, no question, but there was not a huge gap in talent between Iowa State and a fair amount of their opponents (including Iowa). The issue was, for whatever reason(s), Iowa State developed a culture of losing under Paul Rhoads, and that culture had a penchant for showing up when games were on the line last season. In short, Iowa State found ways to lose games against quality opponents (like Oklahoma State) as well as mediocre opponents (like Toledo and Kansas State), so switching schedules with Iowa would have been irrelevant. Again, IMHO.