Preheat oven to 400°F. Whisk vinegar, thyme and basil together in a small bowl. Slowly whisk in olive oil. Place chopped onion, apple, sweet potato, squash and carrots on large baking sheet. Add dressing and season with salt and pepper; toss to coat.
Roast until vegetables are tender and slightly brown around edges, about 35-40 minutes. Place vegetables in a large stock pot and pour in 3-4 cups of vegetable stock, just enough to cover the vegetables.
Heat to medium-high and bring to a boil. Reduce heat to medium-low and simmer 10-15 minutes, until vegetables are soft. Puree soup using a [stick] blender, adding more broth if necessary.
Add yogurt, sugar, cinnamon/nutmeg and cayenne/crushed red pepper flakes and continue to puree until incorporated. Season with a dash of salt and black pepper. Taste and adjust seasoning, if necessary.
Top soup with a drizzle of honey, shaved fresh Parmesan and chopped walnuts/pecans.
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