Preheat oven to 425º. Cut kabocha squash in half and scoop out seeds. Slice into half circles, about 1 to 1 ½ inches thick. Place on parchment lined baking sheet. Drizzle with olive oil and turn the squash pieces to coat with oil. Roast for 20-25 minutes, until completely tender.
While roasting, place fennel, onion, ginger, sea salt, and olive oil in the bottom of a large stock pot and sauté over low heat until browning. Stir frequently.
When the kabocha is done roasting, scoop the flesh out of the skin and add to the stock pot. Add vegetable stock and continue to sauté this new mixture for a few more minutes, allowing the flavors to marry.
Transfer the mixture to a blender and blend on high til fully incorporated. Taste, and add more sea salt as you prefer.
To prepare the dukkah, roughly crush fennel, sesame, cumin, and coriander with a mortar and pestle. In a frying pan or cast iron skillet, gently heat this mixture over medium high flame until the seeds begin to pop, about 1-2 minutes. Remove from heat.
Serve soup with a dollop of plain yogurt, toasted dukkah, a drizzle of pomegranate molasses, and pomegranate arils.