Preheat oven to 350 degrees F (175 degrees C). Line 2 baking sheets with parchment paper.
Whisk together all-purpose flour, whole wheat flour, flax seed meal, cinnamon, baking soda, and salt in a bowl.
Beat together butter, brown sugar, and white sugar in a large bowl until smooth and creamy; Stir in eggs and vanilla. Stir flour mixture into creamed butter mixture until dough is just combined. Fold oats, chocolate chips, cranberries, coconut, and pumpkin seeds into dough just until evenly combined.
Shape dough into 1 1/2-inch balls or drop by heaping tablespoonfuls onto the prepared baking sheets about 2 inches apart; press to flatten slightly.
Bake cookies in the preheated oven until lightly golden at the edges, about 12 minutes. Cool on the baking sheet for 10 minutes; transfer to a wire rack to cool completely.
