Quote from Rquinz
People call me a "kiss-ass". I'm not a kiss-ass. I'm a student that enjoys learning. If I don't like how an instructor is doing something usually it is because I'm not used to doing things their way (even if their way is STUPID). Approach him and tell him that you were complaining because yes you don't like how he is doing things because it isn't how you are used to doing things. Tell him he is a good teacher because he is different but since you've had him it's made you struggle but it's made you grow as a critical thinker. Make him realize what you are complaining about is the material content's complexity and not his teaching (even if it is!!!). He will be more willing to help you especially if you appear honest (and are honest) in your willingness to learn.
I know this post is 2 years old, but the topic at hand is timeless. With all due respect to you (and any student), I do not think it inappropriate for YOU to tell your instructor that you don't like the way he/she is doing things, because its not what you're used to. Even though manners and respect have seemed to fall by the wayside in recent years, I would never dream of being that blunt with my someone who is in a higher position than me.
Be honest and not defensive with him. That will make him have respect for you!!
Honesty is one thing, but diplomacy needs to be considered. Absolutely, not being defensive is key. But to me, saying "I don't like the way you're doing things because that's not how I learned it" IS being defensive. Leaving the first part out of the state to would be the ideal response.