Bring a large pot of salted water to a boil. Add the whole grain fusilli and cook according to package instructions until al dente. Reserve 2 cups of the pasta cooking water before draining.
While the pasta cooks, chop the red bell pepper, snow peas, broccoli florets, carrots, zucchini, and scallions. Mince the garlic and measure out the fresh thyme leaves.
In a large skillet over medium heat, add a splash of olive oil if desired. Add the minced garlic and sauté for about 1 minute until fragrant. Then add the carrots and broccoli florets first, cooking for 3 minutes. Follow with the red bell pepper, snow peas, zucchini, and scallions, sautéing all together until the vegetables are tender-crisp, about 4-5 minutes.
Lower the heat and stir in the cream cheese until it melts and blends with the vegetables. Gradually add the reserved pasta water, stirring continuously to create a smooth, creamy sauce. Add fresh thyme leaves, and season with salt and pepper to taste.
Add the drained pasta directly to the skillet and toss everything together until the pasta is thoroughly coated in the sauce and mixed well with the vegetables.
Serve immediately, garnished with a generous sprinkle of grated Parmesan cheese for that perfect salty finish.