Actually, when made correctly, whole-wheat crusts are not all that bad. The biggest problems that I see are two fold, first, they really should be made from a hard, whole white wheat. This will eliminate some of the bitterness often associated with whole wheat crusts. Second, you need to have enough water in the dough to fully hydrate the whole wheat flour. This generally means a dough absorption of around 70%. The dough will feel soft and sticky at first, but if you allow the dough to rest/ferment/hydrate for about an hour, you should see a significant improvement in the dough as the whole-wheat flour hydrates. Once the dough has hydrated you can ball it and put it into the fridge for some overnight cold fermentation to develop some flavor. With regard to formulation, I personally like to formulate my whole-wheat doughs with higher sugar levels, like up around 5% to achieve a sweeter tasting finished crust. After that, I don't use it for anything but the thinner crust types because I think the flavor and texture might be too much in a thick crust format. Aside from the vegetable toppings, and traditional sauce, or my favorite, slices of fresh tomato to replace the sauce, use a vegan cheese and you should be good to go.
Tom Lehmann/The Dough Doctor