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The entire concept of Knuckles is that he is the Anti-Sonic who is as strong as Sonic is fast. Sonic is like the Flash? Okay, then Knuckles is SUPERMAN, if not ONE PUNCH MAN. Sonic has the Chaos Emeralds to go Super? Knuckles can use the MASTER Emerald to shut down that Super form, if not just flat-out punch it out with sheer brute strength because he is just. That. Strong. Sonic is as free as the wind? Knuckles is the immovable mountain.
The entire concept of Shadow is that he is Dark Sonic. That means he's effectively another Sonic. Chaos Control? Immortality? It doesn't matter what Shadow has. He's another Sonic? So Knuckles can K I L L H I M .
The only reason why this isn't as obvious, is because the image Knuckles has gained in the public eye of the fandom at large is the worst aspects of Donald and Goofy working against himself like the Daffy Duck to Sonic's Bugs Bunny. And in my opinion... Knuckles should never be "Daffy". Because that's obviously Jet.