DH makes my flax 'n' fruit muffins for me.
The RV oven and I DO NOT get along. Plus, he's the better baker. Plain old whole wheat flour is too heavy for muffins, like Vanilla Orchid said. When we can find it, he uses spelt flour. It's available in the bulk bins in a lot of health food stores, many Whole Foods Market locations, etc. When that's not an option, he uses whole wheat pastry flour. Sometimes that's also in the bulk bins, but we have had to buy a five pound bag of it on occasion. So perhaps you could try that before you go back to the white all purpose flour.
It's been ages since he made pizza, but he did made his dough from King Arthur whole wheat flour, the red one pictured here.
http://www.kingarthurflour.com/flours/ It was a yeast dough and needed to rise and all that.