An equal exchange would not work. You need the gluten in wheat/white flour to trap the gas from the leavening agent, or your finished product will be very dense. Substituting 1/4-1/2 C wheat germ/ground flax seed/oat bran for the flour shouldn't effect finished texture too much. The protein powder should be an add in(like nuts or dried fruit) No flour should be left out but you may have to add several T. more liquid.
I make a healthy pancake recipe with wheat flour, ground flax, oat meal, pureed banana, protein powder,yogurt,egg, baking powder and a little water. Some times I will add peanut butter and/or honey. YUMMM!