Preheat oven to 425 degrees F.
Line one large and one small baking sheet with parchment.
On a large cutting board, slice squash in half. Scoop out seeds and reserve. Slice into 2-inch thick wedges.
In a large mixing bowl, toss squash with olive oil, sugar, spices, and fresh thyme. Arrange on the large prepared baking sheet skin side down (so the curves of wedges face up). Sprinkle each wedge with sea salt (using ½ - 1 teaspoon).
Roast 20 - 30 minutes, or until squash are fork tender with golden edges.
Meanwhile, toss squash seeds with olive oil and sugar. Spread on the small prepared baking sheet. Sprinkle with paprika and sea salt. Toast at 425 degrees, with the squash or just after it cooks, for 10 - 15 minutes, stirring every five minutes. Set aside to cool, stirring every few minutes so the seeds don't stick together.
To serve, add crème fraîche to the serving platter, arrange the wedges, and toss with toasted seeds, pomegranate, and fresh thyme.
Though squash is at its best right out of the oven, it can be roasted a day ahead of time and reheated in the oven before serving.