Make the pancakes: Preheat oven to 200 degrees. Whisk together flour, wheat germ, sugar, baking powder, baking soda, and salt in a bowl. Whisk in buttermilk, oil, and eggs. Let stand 10 minutes (if batter thickens, stir in 1 tablespoon water).
Make the compote: Heat blueberries, lemon juice, and salt in a saucepan over medium heat until berries begin to burst, 4 to 5 minutes. Stir in sugar. Simmer, stirring often, until thick enough to coat the back of a spoon, 6 to 8 minutes. Transfer to a bowl, and stir in blackberries.
Coat a nonstick skillet with cooking spray, and heat over medium heat. Spoon in 1 tablespoon batter for each pancake. Cook until bubbles appear. Flip, and cook until golden brown, about 2 minutes. Keep warm in oven while you cook remaining batter. Serve with compote.