To prepare waffles, place flaxseed in a clean coffee grinder or blender; process until ground to measure 1/4 cup flaxseed meal. Set the flaxseed meal aside. Lightly spoon flours into dry measuring cups; level with a knife. Combine the flaxseed meal, flours, wheat germ, sugar, baking powder, and salt in a large bowl; make a well in center of mixture. Combine milk, egg substitute, oil, and vanilla; add to flour mixture, stirring just until moist.
Coat a waffle iron with cooking spray; preheat. Spoon about 1/4 cup of batter per 4-inch waffle onto the hot waffle iron, spreading batter to edges. Cook 5 to 6 minutes or until steaming stops; repeat procedure with remaining batter.
To prepare syrup, combine berries, maple syrup, and ground cinnamon in a saucepan. Cook over medium heat until thoroughly heated. Serve warm over waffles.
Note: Look for flaxseed, a grain rich in heart-healthy omega-3 fats, in health-food stores of large supermarkets. Freeze leftover waffles individually on a cookie sheet and then transfer to a zip-top freezer bag for storage. To reheat, place frozen waffles in toaster.