Can I substitute...whole wheat for all-purpose flour for baked goods?
Whole wheat has more gluten/protein than all purpose flour. This causes the baked goods to have a "stronger/tougher" consistency which may be appreciated in breads, where we want to chew on them, but not in other items like cakes or cupcakes where we want a soft, light texture. In terms of gluten content, in US you can find from higher to lower gluten content:
Whole Wheat flour -> whole wheat pastry flour -> all purpose flour -> cake flour