They're two QBs with different playing styles leading two teams with different offensive systems.
Stanzi, even with all his mistakes, has proven himself to be able to shrug off mistakes and lead the team down the field when it counts. Yes, he's helped out by a good defense, and yes, he's not perfect, but he is a strong leader on the field, and he can make the throws when he needs to. Will his 4th quarter magic hold up? Maybe, maybe not.
Arnaud has had several injuries that have perhaps prevented him from reaching his full potential. He also makes mistakes, but unlike Stanzi, doesn't have as good of a defense to help bail him out. He also doesn't, to my knowledge, have Stanzi's apparent brilliance in the 4th quarter (part of which is apparently forgetting about everything he might have done wrong in the first three...)
What Arnaud has, that I wish Stanzi had a bit more of, is the ability to make things happen on his feet. Yeah, he can move the ball at times using his feet, but doesn't usually do much outside of rolling out on the play action. If he could move the ball even half as well as Arnaud, I think you're talking about a very dangerous Iowa offense.