I have made whole-wheat pizza doughs several times in the past, and have found them to be an acquired taste. The value of the whole-wheat flour is in having a much higher nutritional value than highly refined white flours. They retain the bran, wheat germ, fiber and vitamins (especially Vitamin E) and are metabolized more slowly than the white flours, resulting in a better glucose profile (a concern of diabetics). This makes whole-wheat doughs a good choice for those on high-protein, low-carb diets or those with diabetes. The main problem is getting used to the taste, finding tasty toppings that are compatible with the earthy flavor of the whole-wheat crust, and you are unlikely to get any kids to eat them.
I recently attended a 2-hour baking class on artisan breads that was put on by King Arthur in the Dallas area, and the fellow who conducted the class said that whenever he makes cookies using the KA whole-wheat flour (which is made from hard red winter wheat), his kids won't touch them. When KA came up with a hard white winter wheat version, with the same nutritional value but much whiter in color, his kids couldn't tell the difference from the cookies made with white flour and snapped them up. I don't know which whole-wheat flour you are using, but you can get a good feel for the differences between the two versions at the KA website, at http://ww2.kingarthurflour.com/cgibin/htmlos.cgi/90111.2.1096648561517600069
The whole-wheat recipe I used was the one used by Wolfgang Puck. It is all over the internet, but if you are interested, I would be happy to post it for you.