Preheat oven to 375 degrees F. Spray a 9x13-inch baking dish with nonstick cooking spray; set aside.
Fill a large pot with water and bring to a boil. Add sweet potatoes and boil for 20-30 minutes or until fork tender. Drain the potatoes then place them in a large mixing bowl.
Mash potatoes using a hand mixer or potato masher until you reach desired consistency. Mix in milk, butter substitute, vanilla, cinnamon, nutmeg, salt and pepper until well combined. Spread potato mixture in an even layer in prepared pan.
In a mixing bowl, combine pecans, flour, brown sugar and butter substitute until a crumbly mixture forms then sprinkle on top of sweet potatoes.
Bake for 25-30 minutes, or until topping is golden brown.