Perky, this really isn't that complicated.
ISU struggles against...well, almost everyone, but particularly against other Big 12 teams. This is because the caliber of recruiting/performance across the conference is so high...due in great part to having access to Texas recruiting. Nonetheless, of late, we have beaten Iowa on a very consistent basis...call it 3 of 4, or 10 of 17 if you'd rather...but either way we beat you regularly, and often in your own house.
Still, Iowa manages to win 6-8 games a season...why is this? Well, its because you play one of the easiest schedules in college football in the weakest P5 league in the nation...you have Ohio State and the 13 chumps, 2-3 of which occasionally field a solid team (Wisconsin, MSU, NU). Making it worse, Iowa sometimes doesn't even play these marginally decent teams in the B1G. So you cannot compare records as equal measures...its the head on matchups that tell the tale.
So this all adds up to Iowa State struggling and having weak teams...losing even to some high end FCS schools like NDSU and UNI. Meanwhile, ISU's product on the field is STILL more talented and better than what Iowa is fielding...despite Iowa's ability to put up 6-7 wins against a schedule almost entirely made up of MAC level talent.
Put simply, ISU winning 5-6 games in a Big 12 schedule is equivalent to Iowa winning 9-10 in the B1G. Both teams have stunk these past few years, so in this case ISU's 2-3 wins are equivalent to Iowa's 5-7 wins...this is proven, quite plainly, by ISU's consistent ability to SPANK Iowa in head-to-head matchups.