I perosnally think Shadow will against win Knuckles.
Knuckles does know how to punch hard multiple times,comes from a powerful guardian echidna clan and can use the power of Master Emerald to power himself up,however he is quite dumb and he could easily be tricked by Shadow or any other Sonic villain cough Eggman cough.
Shadow on the other site is way powerful. Not only because he is the ultimate life form created by a devil as seen in STH game,but he also has the Chaos Control, G.U.N orginisation on his side (Seen in Sonic 06), and as well as weapons which he can use handly.He is also quite dumb like Knuckles,however thats just a little bit.Not like Knuckles.
So yea,Shadow takes the trophy.