Place the butternut and acorn squash halves on a baking sheet and bake in a 350-degree oven for about 30-40 minutes or until the squash can be easily pierced with a fork and is cooked through. The acorn squash might need more time than the butternut.
Remove from the oven and let stand while you prepare the rest of the ingredients.
Heat the olive oil in a saucepan. Add onions and garlic and the white wine. Season with salt and pepper.
Cook on medium heat for about 10-15 minutes until the onions and garlic are soft and brown and caramelized. Reserve half the onion-garlic mixture and put the rest into a blender.
Peel off the skin from the squash when it's cool enough to handle. Cut into large chunks and toss into the blender along with the onion.
Add about a cup or more (adjust the consistency of the soup to your liking) almond milk and puree until the mixture is smooth and creamy.
Return the puree to the pan and warm through. If the soup is too thick, you can add some more almond milk or vegetable stock or plain water.
Ladle into bowls and top each bowl with some caramelized onions, garlic and croutons.