That's actually really strange to think about, because outside of a few years around 2008, I've only known Kansas to be bad.
It is more that Kansas State was arguably the worst D1 football program for the entirety of its existence before Bill Snyder arrived whereas Kansas historically was just an also-ran who was generally a .500 team that would have a decent season or two every decade like going 12-1 with an Orange Bowl win in 2007 or 10-2 with an Aloha Bowl win in 1995.
This past decade was the worst one in the history of Kansas football. Right after Mangino left, the Jayhawks had an all-time winning record (15 games over .500). They even had a slightly all-time winning record before his run there, actually.
KSU, on the other hand, has been under .500 since 1947 and had a 28 game losing stream from 1945 to 1948, a couple of 18 and 17 game losing streaks on the 60s.
K-State has definitely had the more successful program over the last 20 years with a whole plethora of 10+ win seasons and bowl success. That and their dominance of Kansas I think makes a lot of folks forget just how bad K-State was for so long. The Wildcats were the Jayhawks of the last decade, but from the mid-30's until the early 90's!
Though I will note I did the math wrong earlier. If the Wildcats win all of the Sunflower showdowns through 2036, they will finally lead in the series for the first time ever!
I think the best summation of the state of the programs is this: The Wildcats have had 8 10+ win seasons since 1997. The Jayhawks have had 4 10+ win seasons
ever. Yet the Jayhawks still have 55 more wins than the Wildcats and only 7 more losses, even after their past decade of futility.