Add 1 tablespoon each of the butter substitute and oil to a large nonstick skillet over medium heat. Add the onions and season with a bit of salt. Cook, stirring frequently, until the onions caramelize, about 15 minutes. Add the sausage and fennel seeds and cook, stirring occasionally, until the sausage is browned on all sides, about 8 minutes. Transfer the onions and sausage to a bowl or plate and set aside.
Add the pasta to the boiling water and cook until al dente, about 10 minutes
Meanwhile, add the remaining 1 tablespoon each butter substitute and oil to the skillet used to cook the onions. Heat over medium-high heat, then add the Brussels sprouts and season with salt and pepper. Cook, tossing frequently, until they begin to caramelize, about 3 minutes. Add the garlic and red pepper flakes and cook for 1 minute more. Return the onions and sausage to the skillet and keep warm over low heat.
Drain the pasta, reserving some of the cooking liquid. Toss the pasta with the Brussels sprouts, onions and sausage in the skillet or a large bowl. Stir in the lemon zest. Moisten with some of the reserved cooking liquid as needed; drizzle with oil if it looks dry. Season with salt and pepper.
Divide the pasta among dishes and serve.
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