Since "those higher level monsters will shake off the worst effects of your casters' best shutdown abilities pretty consistently" rational players simply cease to cast those spells. This leads to fewer choices, a poorer game.
I'm getting the impression Paizo and it's fan base entered collective hysteria. The very notion that a Wizard could ever win a fight by shutting down the big bad seems to fill the Paizo board with outrage and disgust. And this is reflected in the Incapacitation rule.
All this does is drive Wizard players away from using Incapacitation spells, specifically single-target ones, at all.
There's this great mismatch where the game seems to assume you'll still cast those spells even though you could use your high level slots for ... other high level spells? Why would I choose a spell nerfed into oblivion when I can choose another spell, say a damage spell, that isn't?
Inexplicably, Paizo then created a few spells with a decent effect even when the monster does save. This just makes it that much harder to get rid of Incapacitation as the clumsy ugly mechanism it is. Grrr...