Make compote: Heat butter, sugar, lemon juice, and cinnamon in a 12-in. frying pan over medium heat, whisking occasionally, until melted. Add pears and cook, stirring gently a few times, until slightly soft, 5 to 10 minutes. Remove from heat and stir in pomegranate seeds.
Meanwhile, make waffles: Heat a waffle iron according to manufacturer's directions. In a medium bowl, whisk together flour, baking powder, baking soda, and salt. In a large bowl, whisk eggs to blend, then whisk in 2 cups buttermilk, the applesauce, and 2 tbsp. oil. Whisk in flour mixture until smooth.
Cook a small test waffle, coating grids with cooking oil spray if suggested by manufacturer. If it's drier than you like, whisk another 1 tbsp. oil and 1/4 cup buttermilk into batter. Cook remaining waffles.
Reheat compote over medium-high heat and serve with waffles.
*Choose milder and softer whole-wheat flour (such as pastry or Sonora) to heartier (such as hard white or hard red).
Note: Nutritional analysis is per waffle.