Preheat the oven to 425° F. Lightly grease a 9 x 13-inch or 3 to 3 1/2 quart baking dish.
Combine the eggplant, zucchini, bell peppers, onion, garlic, and tomatoes in the baking dish.
1 medium eggplant, 2 medium zucchini, 1 red bell pepper, 1 yellow bell pepper, 1 medium yellow onion, 4 cloves garlic, 4 Roma tomatoes
In a small bowl, whisk together the extra virgin olive oil, tomato paste, water, salt, black pepper, thyme, oregano, and crushed red pepper flakes until smooth. Pour the mixture over the vegetables and toss thoroughly to coat evenly.
1/3 cup extra virgin olive oil, 3 tablespoons tomato paste, 2 tablespoons water, 1 teaspoon kosher salt, 1/2 teaspoon freshly ground black pepper, 1 teaspoon dried thyme, 1 teaspoon dried oregano, 1/4 teaspoon crushed red pepper flakes
Spread the vegetables into an even layer. The dish will look very full at first before the vegetables cook down.
Bake for 45-50 minutes, stirring after 20 minutes, until the vegetables are tender, lightly caramelized around the edges, and most of the liquid has reduced.
Top with the basil and parsley. Taste and adjust seasoning as needed. Garnish with Parmesan cheese, if desired.