Cut the top off of each pepper and remove the seeds and ribs. Transfer to a baking dish. Bake for 20 minutes, until softened.
Heat the oil in a large pot or Dutch oven over medium-high heat. Add the onion and cook for about 2 minutes, until softened and translucent.
Add the garlic and cook for about 1 minute, until fragrant.
Add the zucchini, eggplant, tomatoes, thyme, rosemary, basil, salt, and pepper and stir to combine. Cover, reduce the heat to medium, and simmer for about 30 minutes, until very tender but not mushy, stirring occasionally.
In a small bowl, combine the flour, Parmesan, and oregano. Add the butter and mix with your fingers until the butter has broken down into small pieces and the mixture is crumbly.
Fill each pepper with the quinoa and vegetables, then top with the crumble mixture.
Bake for 25-30 minutes, until the tops are golden brown. Garnish with fresh basil.