First, make the apple cream: combine the crème fraiche, apple cider and cinnamon in a small bowl.
Cover and refrigerate to allow the flavors to combine.
Melt the butter in a large soup pot over medium-high heat.
Add the onions and cook, stirring frequently, until translucent, about 6 minutes. Stir in cloves, nutmeg, cinnamon, allspice, ginger and cardamom.
Cook until fragrant, stirring constantly, about 1 minute. Stir in butternut squash, fennel, chicken stock and apple cider.
Cover, reduce heat to medium and cook until the butternut squash is tender, about 15 minutes. Take from heat and let cool.
Blend the soup in small batches until a smooth puree is obtained. Return to pot and stir in milk and salt.
Bring soup to a simmer. Taste and adjust seasoning, adding more spice if desired. Serve soup with a generous drizzle of apple cream.