Preheat the oven to 375 F (190 C).
In a 9"x13" oven-safe dish, layer the vegetables, beginning with eggplant. Then add the zucchini, garlic, peppers, and tomatoes, drizzling olive oil and scattering thyme leaves over the vegetables as you layer them. Salt and pepper the layers to taste, adding cayenne or jalapeño if desired.
Bake for about 40 minutes, pressing down the vegetables and stirring as they reach the desired softness.
Meanwhile, bring 2 cups of water plus 1 cup of quinoa, with salt and pepper to taste, to a boil.
Cover and reduce heat. Simmer until the quinoa is cooked, about 15 minutes.
Serve the quinoa topped with ratatouille and sprinkled with pine nuts.
Note: The ratatouille can be prepared a day ahead.
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