Heat oven to 450 degrees. Use a fork to prick holes in sweet potatoes; place them on a baking sheet. Place in oven; bake until fork-tender, about 45 minutes. Remove from oven, and allow to cool slightly. Reduce oven temperature to 375 degrees. Cut sweet potatoes in half. Remove skin from one half, and discard. Place potato flesh in a medium bowl. Use a spoon or melon baller to scoop out inside of the other half, leaving skin intact, and add flesh to bowl.
Meanwhile, heat a medium saute pan coated with olive-oil cooking spray over medium heat. Add shallots, and saute until translucent, 5 to 6 minutes. Add 1 tablespoon sage, and saute until fragrant, 1 to 2 minutes. Remove from heat, and place in the bowl of a food processor. Add cottage cheese, salt, and pepper, and puree until smooth. Add to sweet potato, and mash with a hand masher until smooth. Spoon mixture back into skins; sprinkle with chopped pecans and remaining teaspoon sage. Place in an 11-by-16-inch baking pan. Return to oven; bake until hot and pecans are toasted, about 20 minutes. Remove from oven; serve.