The 2002 ISU/Iowa game was just bizarre. So, for me at least, it's hard to make any sort of point based upon that game alone.
However, I actually agree with Lone Clone on the point that it wasn't an upset at the time. For one, and yes there have been plenty of exceptions over the years, Iowa under Ferentz has traditionally gotten better as the season progresses; ISU on the other hand tends to peak in September/early October then as injuries and attrition sets in and they start playing the gauntlet of their conference schedule they start to fall apart. And that is exactly what happened in 2002.
Yes, there have been seasons in recent memory where ISU simply sucked and all of that is moot, but traditionally, at least how I've seen it, that's what happens. And I think that is likely the reason also why Iowa State has had modest success against Iowa head-to-head---and the fact when they have won the game Iowa has usually had a 7 or 6 win season.
All of that said, if any Iowa State fan was honest (or reasonably sane), they would take the success that Iowa has enjoyed under Fry and Ferentz in a heartbeat. Since 2002, Iowa has finished in Top 10 five times, has played in numerous January bowls, has won a fair amount of big bowl games over a handful of SEC teams, has had many individual award winners (Mackey, Outland, etc.), and a long list of other accolades. None of those Iowa State can claim.
So, in conclusion, the big difference between Iowa and ISU boils down to this: Iowa has had Top 10 teams. ISU has not. That's really the difference in a nut shell when you think about it. Because both teams have had plenty of mediocre and bad teams over the years.