Trim the woody ends from the asparagus and cut into 2-inch pieces. Slice the zucchini into 1/4-inch half-moons. Mince the garlic cloves. Set all vegetables aside on a cutting board. Fill a large pot with salted water and bring to a boil—this should be done early so the water is ready when you need it.
Heat 2 tablespoons of olive oil in a large skillet over medium-high heat. Add the asparagus pieces and cook for about 5 minutes until lightly charred and tender-crisp, stirring occasionally. Transfer to a plate. In the same skillet, add the remaining 2 tablespoons of olive oil and cook the zucchini half-moons for 4-5 minutes until golden and charred on both sides. Set aside with the asparagus. I like to char these vegetables first because it brings out their natural sweetness and adds depth to the final dish.
Add the spaghetti to the boiling water and cook for 8.5 minutes until al dente. Before draining, reserve 1/4 cup of the starchy pasta water, then drain the pasta. In the same large skillet you used for the vegetables (no need to wash it—those browned bits add flavor), add the minced garlic over low heat with a splash of the reserved pasta oil, and cook gently for about 2 minutes until fragrant but not browned. Stir in the nutritional yeast and 1/4 cup of reserved pasta water, stirring constantly for about 1 minute to create a silky, emulsified base. This pasta water is crucial—it helps the sauce coat the pasta evenly.
Add the cooked pasta from Step 3 directly to the garlic-nutritional yeast mixture in the skillet. Pour in the fresh lemon juice and toss everything together for about 1-2 minutes, allowing the pasta to absorb the sauce. Season generously with salt and black pepper, then sprinkle in the chili flakes. Taste and adjust seasoning as needed. The acidity from the lemon juice brightens the whole dish, so don't be shy with it.
Add the charred asparagus and zucchini from Step 2 back into the skillet and gently toss to warm through and combine all flavors, about 1 minute. Divide the pasta among serving bowls and top each portion with toasted pine nuts and a sprinkle of fresh chopped basil. Finish with a small tear of fresh mint for a pop of brightness. Serve immediately while everything is warm.