Preheat the oven to 450 degrees . Divide the squash, carrots, sweet potatoes and onions between 2 foil-lined baking sheets. Drizzle 1 tbsp. EVOO over each baking sheet; toss the vegetables to coat. Roast until lightly browned, rotating the pans halfway through cooking, about 25 minutes.
In a large saucepan, combine the roasted vegetables and 8 cups water; bring to a boil over high heat. Lower the heat, cover and simmer until the vegetables are very tender, about 15 minutes. Using a blender and working in batches, puree the soup, transferring pureed portions to a clean pot; season with salt and pepper. (The soup can be covered and refrigerated for up to 4 days.)
In a heavy, medium skillet, heat the remaining 1 tbsp. EVOO over medium-high heat. Add the pepitas and stir until toasted, about 2 minutes. Add the cranberries and sage and stir until fragrant, about 1 minute. Remove from the heat; season with salt and pepper.
Stir the soup over medium heat until it simmers. Ladle the soup into bowls; top with the pepita-cranberry mixture and a sprinkling of pepper.