Which would win?
I think the Darknut and the Iron Knuckle would be at a deadlock, speaking personally. They're both formidable foes to be sure, but they also have their own strengths and weaknesses. It's hard to do this sort of thing, pitting the two greatest enemies in Zelda history against each other and trying to make a decision!
Which would you like to see in the next installment of the series?
Do I have to choose either or? I'd honestly run with both, but maybe I could make off with some super tough
Darknuts in the next installment. I love both enemies with a passion (even made my user title say "ALL ENEMIES ARE DARKNUTS" at one point in time), so choosing either one instead of both is a hard decision.
Were you disappointed they were not in SS?
Of all things within Skyward Sword, the lack of Darknuts and Iron Knuckles made the game feel incredibly dull. I was heavily disappointed with SS due to the lack of my favorite enemies. Sure, they aren't crucial to the Zelda experience, but each and every time they've appeared they have offered me something special. LoZ's Darknuts make quick work of you. AoL's Iron Knuckles will screw you over regardless of if you want it or not -- they're quick and efficient enemies that dispatch even the most skilled of swordsmen.
OoT's Iron Knuckles slammed their axes into you, ensuring you lose at minimum four hearts.
MM's were much the same, with an added speed boost if you manage to crush their armor.
TWW's Darknuts are excellent swordsmen as well as having CQC under their belt.
TMC's Dark Knight was a formidable foe that I enjoyed fighting and refighting.
TP's Darknuts managed to corner me int he Cave of Ordeals, screwing me over time and time again. SS's just didn't exist, to my chagrin. Again, they aren't essential to the Zelda experience, but having them in does nothing but good to me.
I think the Iron Knuckle would win. It's attacks do more damage to Link to begin with, and to top it off they're harder to beat. In TP, you can just spam the Helm Splitter and the Back Slice and they're dead in no time. With Iron Knuckles, it's always risky to get close to them, and there isn't a fast way to defeat them.
In the games where the Iron Knuckle does less damage, the Link in question has little to no protection. It's only fair he takes more damage. In Twilight Princess, our hero in green is a veteran swordsman who takes skills that his ancestor -- the Hero of Time -- teaches to him in no time flat (probably in a hyperbolic time chamber-like area, too). It's only fair that he can dispatch enemies so easily.