Snyder's stubbornness made him a very good coach, but it also kept him from ever becoming a great one.
Snyder was insistent on doing things his way. As a result, he never tried to upgrade KSU's overall talent base to include more four star prospects. That meant that even as the rest of the conference upgraded their coaching staffs, he never upgraded his talent to match theirs. Look around the Big 12 now. Where does KSU have a distinct coaching advantage? I'd argue that they don't have a significant advantage over anyone other than KU. And with KSU's talent deficit, that makes winning in conference pretty tough.
Add to that the fact that college football has changed over the last 30 years.
When Snyder started at KSU, you could schedule four non conference games and play your other seven conference games. If you scheduled four easy wins, you could go 2-5 or 3-4 in conference and still advance to a bowl. Then it was 12 games, but the same four non conference, with eight conference games. You could go 6-6 and make a bowl. Snyder took full advantage of this. Excluding his first year when the team went 1-10, Snyder's teams lost seven regular season non-conference games between 1990 and 2005. That's 16 years. Snyder basically scheduled himself four guaranteed wins just about every season.
Snyder still doesn't lose many non conference regular season games now (seven more over the last 10 years), but he only gets three non conference games now instead of four. On top of that, he's no longer coaching in college football's desert, having weak programs at KU, MU and Iowa State to regularly pick up wins against. When Snyder started, he had seven wins on his schedule before he played a single game (maybe eight when Oklahoma State was down). Now, he has three or four. He has to scuffle to get bowl eligible. And in three of the last four years (including this one) KSU has had to scramble down the stretch to get enough wins to get bowl eligible.
Snyder can't schedule his way to a bowl (Big 12 put pressure on K-State to schedule stronger non conference opponents or be shut out of the early season TV schedule), so he has to have a P5 team on the slate. He can't pick on anyone in conference (other than KU right now). There's no clear path back to success for KSU because Snyder's blueprint depended on scheduling weaker opponents in non-conference and honing his execution against teams that couldn't blow him off the field with talent. Without that, Snyder is stuck.
This was always how it was going to end for KSU. Snyder elevated their win total without ever elevating the program. It was a mirage of success built mostly on the struggles of other programs around him. It's time to pay the piper.