Heat oven to 350°F and prepare two large baking sheets with parchment paper or silicone baking mats (NOTE: Cookies made on silicone mats will spread more than those baked on parchment).
Mix 2 Tablespoons ground flax seeds and 1/4 cup water together in a small bowl. Set aside for at least 5 minutes.
Stir together 2 cups whole wheat flour, 1/4 cup brewer's yeast, 1 Tablespoon wheat germ, 1 teaspoon baking soda, 1/2 teaspoon baking powder, 1/2 teaspoon salt, and 1/2 teaspoon cinnamon in a large bowl. Set aside.
Cream 3/4 cup (1 1/2 sticks) unsalted butter, 1 cup brown sugar, and 1/2 cup granulated sugar together in a stand mixer fitted with a paddle attachment on medium-low speed. Add 2 large eggs and 2 teaspoons vanilla extract and mix until completely incorporated. Add the flaxseed mixture.
Reduce mixer speed to low and slowly add the flour mixture. Mix until incorporated. Add 2 1/2 cups rolled oats and 1 cup chocolate chips.
Drop 1 Tbsp portions of dough onto prepared baking sheets 2" apart. Bake 8-10 minutes, until edges are just beginning to brown, but middle is still quite soft. Cool on baking sheet for 5 minutes before transferring to wire rack to cool completely.
Store in an airtight container or bag at room temperature for up to 4 days or in the freezer for several weeks.
Notes
Substitute an equal amount of chopped nuts or dried fruit (or a combination of any of the three) for the chocolate chips if desired.