Place sweet potatoes on a large baking sheet or cast iron skillet. Drizzle with 2 tablespoons oil, and sprinkle with salt and pepper; toss to coat. Bake at 450° for 30 minutes or until tender, turning after 15 minutes.
Place remaining 1 tablespoon oil, cranberries, water, honey, and chipotle paste in a saucepan. Place pan over medium-low heat; bring to a boil. Cover, reduce heat, and cook 10 minutes or until cranberries pop, stirring occasionally. Remove from heat. Mash with a potato masher or back of a wooden spoon until chunky.
Place pepitas in a medium skillet; cook over medium heat 4 minutes or until lightly browned, shaking pan often.
Combine potatoes, pepitas, onions, and cilantro in a bowl. Add cranberry mixture to bowl; toss gently to coat.