Heat the oven: Preheat to 400°F (200°C). Lightly oil a 9x13-inch baking dish or similar casserole.
Build the tomato base: Spread the crushed tomatoes in the dish.
Stir in half the garlic, 1 tablespoon olive oil, a pinch of salt, and a grind of pepper. This keeps the veggies juicy.
Prep the vegetables: Toss eggplant, zucchini, squash, peppers, and onion in a large bowl with the remaining olive oil, garlic, thyme, oregano, paprika, red pepper flakes, salt, and pepper.
Layer and bake: Arrange the vegetables over the tomato base. For a rustic look, scatter them.
For a prettier finish, shingle the slices. Cover tightly with foil and bake for 25 minutes.
Uncover for caramelization: Remove foil and bake 20–25 minutes more, until the vegetables are tender and edges are lightly browned. If you like a bit more color, broil for 2–3 minutes at the end.
Cook the quinoa: While the ratatouille bakes, bring broth to a boil.
Add rinsed quinoa, reduce heat to low, cover, and simmer 15 minutes. Turn off heat and let sit, covered, 5 minutes.
Finish the quinoa: Fluff with a fork. Stir in olive oil or butter, parsley, dill or basil, lemon zest, lemon juice, and black pepper.
Adjust salt and lemon to taste.
Finish the ratatouille: Let it rest 5–10 minutes. Sprinkle with fresh basil or parsley. Add a drizzle of olive oil or a dusting of cheese if you like.
Serve: Spoon herbed quinoa into bowls and top with generous scoops of ratatouille.
Add a squeeze of lemon or a few chili flakes for brightness and heat.