Preheat oven to 450°F.
Seed the pumpkin and cut it into 2-inch pieces.
Peel and cut the sweet potatoes into 2-inch pieces.
Combine the pumpkin, sweet potatoes, and garlic on a baking sheet, toss with 2 tablespoons of olive oil, and sprinkle with salt and pepper.
Roast in the oven until the pumpkin and sweet potatoes are tender when pierced with a knife, about 30 minutes, tossing halfway through. If you left the pumpkin skins on, peel when cool enough to handle.
Heat remaining tablespoon of olive oil in a large pot over moderate heat. Add shallots and ginger and cook until softened. Add miso and vegetable stock and stir until dissolved. Add roasted vegetables and simmer for 15 minutes. Turn down heat if necessary to avoid boiling, as this can impair the flavor of the miso.
Puree the soup using an immersion blender, or puree in batches in a blender or food processor.