Milk proteins change with the pasteurization process. Pasteurization heats milks to between 149 - 161 (my best understanding). Using raw milk, the milk (usually) gets up to 100 F at most in the cheese making process. I believe that the effect of the heat accounts for the change in the flavor, but what do I know? In addition using pasteurized milk requires more rennet, more culture and the addition of calcium chloride. I'm not sure if this is a factor or not.
Interestingly (to me, anyway) raw milk can be clabbered. This is the simplest way to get a sense of the complexity raw milk cheese has, by comparing clabbered milk with commercial sour cream or buttermilk (but don't try to clabber pasteurised milk, it's dangerous).